There is one reason to evacuate the population even if there was no danger of genocide: The need for work force. It can be assumed that the majority of the Caldari population was on Caldari Prime, but - now that the planet could be blockaded by the Gallente - suddently the majority of the industrial sites necessary to fight the war were on the colonies.
Looking at the rank quotes:
The Federation is not a defined region of space, of planets, of mountains, rivers, or woods. It is a vision.
- President of the Federation, Arlette Villers. CE 23154.6.2
Things start to roll on early June.
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 Kaalakiota CEO Matias Sobaseki. CE 23154.6.26
Caldari don't seem to be very happy. This from late June.
The laws of the Federation were written for the good of the many. Not the good of the Gallente nor the good of the Caldari. Hopefully, we can help them remember this.
- Gallente Senator Fronte Belliare, Senate session 23154/T3782. CE 23154.11.21
This may or may not coincide with the secret colonies being discovered and the Federation wanting control of them.
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
In any case, during the five months, debate has heated up.
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
...and there we go. At least five months of discussion, and Caldari secede.
You have long since made your choice. What you make now is a mistake.
- Excerpt from the Federation Presidents response to the Caldari Proclamation of Secession. CE 23154.11.22
The Federation, as we know, doesn't accept the secession.
They seek to fragment the Federation for their own selfish pride. Take their planet, strangle it and let's see how proud they stand after.
- Vice Admiral Eisen Piroit, Addressing the Senate. CE 23154.11.28
After a week, the Federation Navy uses blockade...
We survived on this world for thousands of years without the Gallente. Do they think we will starve now?
- Wiyrkomi CEO Taaiko Wiyrkomi, Response to the Gallente blockade of Caldari Prime. CE 23154.11.30
...it's not very effective.
They will retaliate. We must be prepared.
- Vice-Admiral Orlan Mito, Caldari Navy, Morning after the Nouvelle Rouvenor attack. CE 23155.1.14
After one and a half months of blockade, Nouvelle Rouvenor happens.
A moment of silence is not enough. For their crimes, we must make the Caldari silence permanent.
- Luc Duvailer, newly sworn in President of the Federation, after the Nouvelle Rouvenor attack. CE 23155.1.15
The Ultranationalists seem to be A-OK with genociding some Caldari.
[04:00][Command] Orbital Bombardment to begin T minus one hour
[04:05][Command] Fleet begin deployment into close orbit
[04:40][Command] Begin Lock Targets. Orbital spread. Pattern Delta-Four-Two
[04:59][Command] Admiral Signals: For the people of Nouvelle Rouvenor
[05:00][Command] Authorize weapons free. Execute bombardment
- Fleet Log, Caldari Prime Orbital Bombardment. CE 23155.1.17
First strike seems to follow some pattern.
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
However, there seem to be a significant amount of survivors. This would seem to signal a change towards total warfare.
As we make the tea, you must take it. The Caldari way demands it.
- Matias Sobaseki, CEO of Kaalakiota, Morning of Reasoning. CE 23155.2.10
This far, there has been those corporations amongst the Caldari who have supported staying in the Federation and opening negotiations. After Caldari Prime has endured the siege (and assumably bombardment) for over three weeks, the Morning of Reasoning happens.
The savages have murdered the only ones with any sense among them. They lit the fire, now they will burn in it.
- Senator Fronte Belliare, Morning of Reasoning. CE 23155.2.10
The Morning of Reasoning seems to have intensified the conflict even more.
This Federation is now at war. We have no time for dissenters, our Admirals will follow the will of this government or we will replace them.
- Hume Roir, newly appointed Gallente Minster of Defence. CE 23155.2.18
A week after the Morning of Reasoning, the Gallente seem to have some war weariness, but the U-nats are still in control.
Their fleet is in total control of Caldari Prime's Orbit. We're heavily outnumbered and outgunned. To be able to effectively evacuate the population we need exactly one month of complete orbital control. Ideas anyone?
- Admiral Orlan Mito, Caldari High Command Session. CE 23155.2.21
Evacuation of the population starts almost two weeks after the Morning of Reasoning. Bombardment has lasted for four weeks and the siege for over eleven weeks. The Breakout chronicle tells us that the Caldari need one month / four weeks to evacuate. The Caldari counterattack drives the Gallente from the orbit and there's even talk about bombing Gallente Prime.
High command need more time to complete the evacuation. We shall provide.
- Admiral Yakiya Tovil-Toba’s personal log entry #21A231. CE 23155.3.7
Four weeks after the Morning of Reasoning and little over two weeks into the evacuation. The Breakout tells us that initially, the Caldari were successful at taking control of their orbit. About half of the Caldari population is still on the planet, and the Federation is ready to counterattack. Tovil-Toba disrupts the counterattack by attacking the Gallente ships and facilities on the orbit of Gallente Prime.
He is a cunning one this Tovil-Toba, but he can not evade us forever and his destruction will serve as an example to all Caldari.
- Admiral Eisen Piroit, Gallente Navy. CE 23155.3.10
Initially, the campaign was quite successful, but Tovil-Toba's resources are few.
Non-essential personnel, abandon ship.
- Admiral Yakiya Tovil-Toba’s last command. CE 23155.3.15
The evacuation is almost complete, but the fleet under Tovil-Toba has been destroyed. We know what happens.
Hueromont was our failure yes - our failure to strike harder and strike faster to destroy those traitorous bastards where they stand.
- Luc Duvailer, President of the Federation. CE 23155.3.16
Despite the Ultranationalist words, Tovil-Toba's last action caused a change in government for the Gallente.
...and of Caldari bloodlines, I cannot remember chrons either, but essentially, the lack of other bloodlines from Caldari Prime has been hand-waved as the bloodlines being assimilated into Deteis and Civire due to them being minority groups in the new post-evacuation colonies.
Edit: Fixed one quote. (Tags instead of quotation marks.) Quotations collected from Caldari and Gallente militia rank descriptions.