It would prevent players to be kicked out too fast, because currently a 'game' lasts as long as it takes to destroy the emp without any interference (let the allied guild attack it freely). The only two reasons, why it might last longer is to allow one guild to take a certain fortress first or if one guild got a sufficient occupation score already. The first goal is assured by dropping an Emp below 50%. In that way, it doesn't matter if someone else manage to destroy it, the owner is still determined by the majority of the damage dealt.
The only real question is: How such an ally system should look like. (the devs will ruin it nonetheless).
As attractive as an alliance system seems atm I doubt it would fix anything. I would just tell coli not to ally with us. Have them ally with blood order/gala and we do the same then just continue the swap while hoping that gala/blood order alliance helps them in the cluster-_-fest that is known as taking south fortress. The objectives are just entirely too easy to take atm...in the future yeah it would be nice to just forge your alliances legitly and defend stuff, but as is now there is really no point. Atleast imo there isn't