Will Michael join CJ's team or...

[Cabbage Patch]

...he has a crew of soldiers around him who seem to follow his order. But would they follow him, if he leaves; would they allow him to leave the armless Colonists behind?

Good point. I think Puck, Carl and Riley (can't forget she's a soldier too) are personally loyal to Michael, but Roberts and Muldoon just met the guy. How far do the bonds of military discipline stretch when the military, and the nation no longer exist?

...When he stays, he will do, what he did during his time with Kimmet: He will follow his personal agenda as much as it is possible - especially with CJ not knowing.

CJ isn't Colonel Kimmet. She's detail oriented, a micro-manager, she seems to crave power and control, and she holds grudges. Kimmet seemed like he was resigned to his fate, like he was only going through the motions, while CJ is a fighter. I don't think Michael would have the latitude to get away with nearly as much under CJ, and if he tries too hard I believe that CJ isn't above arranging a "Sean-type accident" for him.