Long story short Jamyl as portrayed in the 'novels' is more of a 'tortured soul' fighting with being possessed by dead ancient beings, drug-induced lesbian daliances, and, and whining about not wanting to be the Empress.
God-Empress of a trillion devoted holy-warriors she is not.
As I said, the Tony G books aren't counted under EVE background by me, my chars don't know 95% of the stuff that happened in them anyways, so why should I bother? Also, I think she's not supposed to be God-Empress (That's a Sabik thingy), but rather Caesaropopess.
That's the rational part of your brain talking. If they thought like that the State wouldn't have rolled the entire fleet dice on retaking Caldari Prime, the Matari wouldn't have invaded the Empire, etc.
Ambition and rationality don't always go hand in hand, as most rational people wouldn't willingly kill millions of people to get a little more territory, wealth, and status.
And I think history shows that even though there are episodes of irrationality, most of how it went is subject to rational interests of nations, that go about reaching them in a rational kind of way. Nations don't have ambitions, they have interests. The Caldari retaking of Caldari Prime and the Matari invasion of the Empire (though both had imho their rational elements - though not necessarily from the point of view of the respective political entities, but from the point of view of those grabbing for power within those political entities - people that had ambitions) were bouts of irrationality enough. All out war would just go against my suspension of disbelief.
Also, killing millions of people for a bit more territory, wealth and/or status might very well be the
rational thing to do, imho, if the gains outweigh the expected losses. It might not be
reasonable to do it anyways, but there is a difference between 'rational' and 'reasonable'. The Nazi's were all in all quite rational and effective in what they were doing, unfortunately they weren't quite that reasonable.
Also, as Lyn pointed out, it's a situation that limits RP more and more within and agmongst the 4 main factions of EVE and as such I think it's a bad thing.