Which part of the PF does support the notion that the Federal Government was being at all malicious in it's actions?. The timeline says the Caldari (I wish CCP had made the distinction between the governments and the races more clear ) were forced to join the Federation by circumstance, not by coercion.
Circumstance implies coercion or threatened coercion. Precisely how else would the Caldari be "forced" to join? It's made fairly clear by the timeline that the Gallente were rapidly expanding, assimilating all nearby planets and populations. Therefore, since they lacked the technology to resist, the Caldari had no choice but to join, either peaceably, or, eventually, by military subjugation. This is not unreasonable: consider the fate of colonies and tribes that stood in the way of the Westward Expansion of the United States.
If 'Caldari' means all Caldari, then IMO the specifics become quite muddy, why would all 'Caldari' agree to join on circumstance? The proto-Fed would sway to the masses as much as it does today. But if 'Caldari' means the ruling corps (as I think) then it makes sense they felt forced to join either by their affiliations with other corporations and governments or because the broader populace was okay with the Federation. Either way the corps did join the Federation, so why would the Federal Government think all Caldari felt unhappy or disaffected by the decision, if the average Joe even did feel unhappy at the time.
It's noted in the Corporation descriptions and the Chronicles dealing with them that the Megacorps essentially
were Caldari society and government well before the secession. But to assume that the Megacorps had such a role at the time of the Federation's founding is an entirely different matter, and, moreover, the beginning of the "The Early Days" Chronicle states that the corporations were not as powerful as they are now. Nonetheless, this point has little relevance to the discussion, I think.
The chrons state that once the Federation stumbled upon a secret colony, (noting that reach of the Federation wasn't even enough to find out about millions of people and a secret military), they did what I imagine any government would do, and asked for the colonies to be put under their control. The next line of the chron is: "This was too much for the Caldari Corporations, which were already grumbling over increasing Federation interference into their affairs." (Emphasis Mine) I don't think it is at all unreasonable to say that the corporate leadership led the succession not because of any bold Braveheart-esque notions about freedom from tyranny, but simply because their bottom line and ability to operate freely was being hurt by Federal taxes and regulations.
Your assertion that the rebellion was not popular in nature is contradicted by numerous sources of PF (again, by my reading):
"Slowly but surely we are betraying the legacy left to us, the children of the Raata. The light of the Caldari spirit grows ever darker under the encroaching shadow of our would-be masters. Our very identity as a people is being subsumed by the Federation and we must act to preserve it."
- Excerpt from a National Address, delivered by Kalaakiota CEO Matias Sobaseki. CE 23154.6.26
"It is rather strange that the good of the many seems to constantly coincide with whatever policies weaken the Caldari, the Intaki, and the Mannar and keep them under the heel of the Gallente."
- Caldari Senator Kiriusu Otenga, Senate session 23154/T3782. CE 23154.11.21
"We will not permit you to tell us how to be Caldari, and so you leave us with no choice"
- Excerpt from the Caldari Proclamation of Secession. CE 23154.11.22
The Caldari never wholly clicked with Gallente government. Even when they were co-founding the Federation alongside the Gallente, Intaki and Mannar, the Caldari megacorps were also establishing secret colonies and deep-space resources outside of Federation borders that weren't subject to Gallente trade regulations. The Caldari viewed this as part of the process of retaining their cultural identity and autonomy.
So, we have a quote from a Caldari CEO, a Caldari Senator, and, presumably, one from whatever Caldari government existed at the time. In addition, from "The Early Days" we have Caldari guerrillas and partisans, in addition to the terrorist dragonaurs. We should also keep in mind that executing a war is the worst thing a corporation can do to its bottom line, since military forces are an investment with no material return (narrowly speaking). As well, there were corporations that did not want to secede, lending further credence to the point that the conflict was not economically motivated. A broad-based, economically disastrous war for independence has, in history, usually been the result of popular feeling and mistreatment of the rebelling population.
As far as genocide goes, burning cities don't prove anything, this is Baghdad in 2003: http://www.youtube.com/watch?v=T0kcaziP-0o and lot of Iraqis probably won't like the coalition for a while, but doesn't mean any genocide was attempted during the Iraqi war.
Fortunately for Baghdad, we weren't bombing it from orbit, or the results would have been, ah, different. Consider the other sources regarding orbital bombardment that we have in Eve, if you will. First, the Starkmanir tribe was nearly destroyed by an orbital bombardment (Chronicle: Khumaak). The Sansha were nearly annihilated by similar means. The Chronicle Xenocracy has a capsuleer threatening the destruction of a city by means of railguns. The specifications are exact: each shell will destroy everything within half a kilometer. The only orbital bombardment in Eve history that is not totally catastrophic is the Caldari bombardment of Caldari Prime in the invasion, and those bombardments are said to have been directed as pinpoint strikes against purely military targets, and they still lead to massive loss of life.
Genocide isn't necessarily wiping out every member of a race or people. It's the destruction of massive numbers of them, usually only for the crime of being in that group.
Secondly given that there was a large Gallente population on Caldari Prime (supported by the chrons) indiscriminate bombing would be killing a lot of them too.
Well, we may presume that it did, although, since the Gallente apparently preferred underwater cities, perhaps not.
Thirdly an entire population of I'm guessing hundreds of millions (I'm not sure on the numbers) into the wilderness? I know the chron says it but it strikes me as completely implausible if they were fleeing orbital genocide. In order to support that many people we know from modern experiences they'd likely end up in large refugee camps, which would be perfect targets for orbital strikes. And if they didn't, how exactly would all these city dwellers survive in small groups without survival gear and supplies? I think it's more likely that some of the population fled because of the bombing and invasion, but not all of it. Finally if the Federation really wanted to commit genocide, why bother invading? Just evacuate as many of the loyal citizens as you can then drop NBC weapons onto the population centers. Remember the Federal government at the time was massively pro-war and anti-Caldari, with the doveish elements terrified of being 'traitors'. And the Navy officers were newly appointed cronies, I'm sure they would have been willing to kill Federal citizens as collateral damage ("They will sing songs of your sacrifice" or "They lived on the same world as the Caldari! They were bad!").
Again, you are contradicted (in my opinion, based on my reading) by both real world history, and by PF.
First, consider Germany's approach to genocide in World War 2. Why, if they wanted the Jews and the Russians dead, would they bother invading? Well, partially because they wanted the land (and similarly, apparently many Gallente preferred to live on Caldari Prime) and because genocide is difficult to accomplish from the air alone. Very difficult, in fact. As well, the germans desired to use the russians as slave labor and serfs. That the Gallente would plan to eventually put boots on the ground to assure their victory isn't unreasonable - it's actually necessary for the aim.
Second, from the "The Early Days" Chronicle:
...the Federation retaliated at once by sending an invasion force down to Caldari Prime and began a systematic orbital bombardment of the planet. Soon, the Caldari population had been driven to the mountains and the forests; their resistance getting weaker by the day.
Now, systematic doesn't mean "targeted at military installations". It means "thorough", "complete", and "methodical", to take a few from a thesaurus. And the Chronicle states that the remaining Caldari population were driven to the mountains and forests. Not the military (which was apparently only in the colonies anyway), but the civilian population. If we examine under what circumstances this occurs in a war, we see (consider Japan and Germany in World War 2) that it happens when cities are completely destroyed (as in the firebombings). If civilians are able to remain, they typically do (as in the Blitz).
In addition, if the Caldari civilian population was in no danger, than the decision to evacuate them was insane. Left on the planet, they'd cause far more trouble for the Federation than they would cause the military of the nascent State. Evacuating them nearly cost the Caldari the war - why the need for so hasty, dangerous, and foolhardy an operation? The only explanation to hand is that the Caldari population faced an existential threat.
To end, the following quote puts the capstone on my argument for the bombardment being targeted at the civilian population:
"Caldari Prime burns, those left behind are choking on the dust and ash that fills the air, and you demand our surrender? Is this a joke? You have only hardened our resolve. Every drop of blood you have taken from us will be repaid -- with interest."
—CEP response to Federation demands for unconditional surrender after initial bombardment of Caldari Prime. CE 23155.1.18