I think that bringing the Mollies into the fold is a VERY good idea.
British history is replete with examples of ex-colonies gaining independance when they kick up enough of a stink. We are good at being embarrassed about our colonial past! So I don't see why this shouldn't follow through into the FL universe.
Also, with the increasing hostilities around the omega's we could do with the help!
Relations should obviously be decidedly frosty to begin with. Perhaps the odd engagement with associated finger pointing (You started it. No I didn't, you did! etc). Gradually warming to possible joint actions. Certainly the QCP originally had a policy of "Don't shoot us and we won't shoot you" with the UoG when we started up.