Wouldn't the 'victor' know of a small band of rebels/terrorists/freedom fighters? He would just hunt them down. For which reason I don't think it would work. Also, most players would just abandon their particular team at that point and start afresh; another reason why it wouldn't work.
Sorry but I can't see it actualising. I think the team would be a lot more strict. Plus, it has to remain an RTS, at most, with RPG elements.