I think the significance of the civilian thing for me, is how it speaks to Jack's intentions regarding Sam. Resigning from the AF would be a huge deal for him and I can't see him taking a civilian command lightly. So if he has done and taken Kerry's advice, it tells me that he's serious about wanting to begin a relationship with Sam and that that's the most important thing in his life, rather than his career. Which would be big deal for this character, I think.
Although, having said that, just realised that he is wearing his AF uniform in the trailer for Origins. Course, could be from a Mitchell flashback, I guess.
LabRat
(getting more eager to see next week's episode by the minute
)