You know, that was actually sounding kind of promising up until the "But is Rush telling the truth?" part.
I think that may just be Carlyle covering a bit for having given away most of what happens in the first half, not that Syfy's trailers don't do that already.
I prefer them working together. And Rush had really changed in the last few episodes of the season--at peace with himself.
As on Voyager, continuous infighting is ridiculous when there's an external enemy or plain survival is at stake. It gets monotonous. Provided the "working together" is built up to, it shows growth in the characters. When not built up to, it shows lazy writers and idiot networks/producers.
Voyager was a bit too quick to make everyone friends, but you are right the constant fighting among the SGU characters is getting tiresome.
Atlantis actually handled this somewhat realistically in its first season. For the most part everyone worked together peacefully enough, with notable exceptions. Things like Dr. Kavanagh whining about Weir, Teyla and Sgt. Bates always at each others throats and McKay getting pissed at everyone.
Let's face it, no matter the circumstance there's always going to be people who don't get along with someone.