There would be no change necessary in this regard, as we already have the rule that you do not get any war perks if you were part of the winning team for less than 12 hours.
Hmmm. Do you think 12 hours in enough? If one side starts to get momentum, then may folks might switch to that side to cash in, rather than fight in a losing effort. This incentive could force many lopsided contests with folks switching early to the side with an edge, and then it becoming a tidal wave.
Do you think a modification to the rules determining side are in order? Perhaps a is a side has a sertain lead based on your point system, folks who switch to it don't qualify for perk points. I think some modification will be necessary. but I like the idea.