I'd say some sort of an existing tiff between Gates and Larissa is probable, with Hammer perhaps being a one-up on his part. But the reference he made to his crew on the last page has me wondering a bit. Also, I'm not sure I get the point of making Hammer strip before releasing her. Well, aside from the obvious, that is.
Edit: You might be right about Gates's angle on this. Based on
Page 37/7, Gates seems to have lost some support amongst the Kids faction (your "regular Colonials", I assume) after the battle of Risae. According to my take, based on what we've seen here, Larissa is the biggest threat to his authority at the moment. The Kids and the Mercs might be influential, but it could take either of them a long time to go against the chain of command and organise themselves around one of their own leaders to cause troubles for Gates. Whereas Larissa has a built-in separate power base in her own crew, who are used to taking orders from her. So perhaps Gates is trying to provoke her into doing something inprudent, while military discipline still outweighs his leadership shortcomings in the minds of the two other factions.