It's called growing up. The longer you work for the government the more you become like the government or man in this case. I know because I have worked for them going on 16 years now. No person stays the same in the real world. We all grow or we stagnate as a person.
Some truth in that, yes, but also, it's a serious break from established character...more than could reasonably be expected in a 3-4 year period...even the O'Neill in "Continuum" was more Jack than the one we're seeing in SGU. I don't think all of it can be due to "growing up".
I too worked for government for 23 years and then went into private business. Certainly, from 22-45, I grew up and changed substantially. I think most people would. But going from 45-49, I don't think I've changed that much more.
My point: unless the timeline has advanced significantly in SGU from where it left off in Continuum, I think it would be more realistic if O'Neill were more like the Jack we knew (even in Continuum) than the one we're seeing in SGU. Simply: the writers (or execs at Sciffy...or both) are seriously departing from established thematic elements and I think the show is suffering because of it...
Presently, I find myself enjoying Sanctuary quite a bit more than SGU, and I never expected that to happen...