I think my only concerns are already addressed. I wouldn't want to see company assignments "locked in", but you've already stated that they're only locked in for a single contract. I do think it might lead to some circumstances where you consistently never fight cooperatively with some players, especially if your lances are similar in function and therefore constantly get split between two different companies. Personally, I'm of the belief that mixing up forces keeps the group harmonious. If you're always on the opposite side of the table from the same players, it can lead to grudges and hard feelings.
I'm a little worried about the potential to crash the campaign, but as long as you're confident you can fully restore w/o incident then no problem. We've built a good story here, so I don't want to see it wiped out.
As for the potential positives ("which means it becomes possible for one Company to start getting really screwed over under several sets of circumstances"), haha, that sounds awesome. I've said before that we've been too good, too rich, and too customized for my taste. At this point, we're an elite merc unit because we NEVER LOSE. Sure, we've taken some materiel losses (mechs, pilots), and we've had the occasional minor contract breach, but nothing major. We haven't ever said "screw the contract, if we don't pull out now, we're all toast". We haven't ever had a situation where 3 lances get so thoroughly crushed during an engagement that we have to come together as a unit and figure out how to turn them back into effective fighting forces. Most people's longest downtimes have been related to installing the newest shiny on their Jaime-Wolf-wannabe ride, and quite frankly we're bigger Mary Sue's than the FedSuns at this point.
(don't get me wrong, the campaign is awesome and I'm having a blast)
My point is... yea, fine, take the gloves off. If this means there's a chance the story gets more interesting, I'm all for it. (^_^)b