Vanilla is a product of Lussumo:
Documentation and Support.

being instrumental to the destruction of the Ressurection Ship

Tearing people apart, making the "right" decisions ugly and wrong, that's good drama.
religious fanatics to win
So, yes and no, I think what the writers know of Israel/Palestine informs their understanding of the conflict in their show, but no, I don't think it was a direct inspiration for that conflict.
My quibble is tossing in the lip-licking rapist types on Gaeta's side.I think part of the point is to show that those types will end up on any side. If that guy was in it for good-intentioned philosophical reasons, he'd just want to execute Sharon and be done with it. But no matter how noble a cause is, there are always people on both sides who only want an excuse to fuck people up.
In the end, to me, conscious allegory almost always cheapens the thought behind a story. It turns what could be a genuine exploration of something human into a simplistic puzzle of what make believe thing is meant to equal what real world thing. It also carries some presumptions that the author of the allegory is somehow above the real thing and able to make these allegorical judgments of what is really going onTwo words: Animal. Farm.