Re: Chapter three
Aye, none of the Marines really "worship" the Emperor, or at least most of them seem to understand he isn't a God. He's their creator, and he's the progenitor of the Imperium, but he's not a god.
As for the portal, I'm fairly sure that, if it were in Calixis, they would have mentioned it in the fluff. Now, the Koronus Expanse... anything could be in there, and it'd explain how the hell the Kroot managed to turn up from the opposite side of the galaxy.