This is a worrisome issue, indeed. But if they do that, then it will become known to the other team to not bother attacking it, if it's clear that they will loose it. Thus that team will just ignore it and force the original team to finish it off to actually get the points. And this will result in them being distracted from the other bosses. Which will help the other team to get that kill.

But I believe I have a solution to this issue.
What if the kill was actually based on the team that was hammering it? Kind of like the Strongholds/Territories game-type? But instead of being in the radius of the flag, the teams simply have to shoot at the boss until he goes down. There be no indicator as to his health, but one that resembles the stronghold territory. Instead of a life bar, it's a bar that shows which team is getting the most hits in. And as it fluctuates, the teams must then work together to finish the boss off. Basically a Tug Of War between teams for each boss. And while they are trying to win this mini war, they are all being shot at by the boss, A.I. minions, and the other team. Of course, which ever team has the most powerful shots, will fill the bar more with their color. This way, a single player or two has a chance to stall the opposing team's boss win until his backup arrives. Then it becomes a all out tug of war fight. Just like the base captures. It may take a while, but eventually one team will win.

In case all of that came out too complicated, here's the short version.
Make Boss fights play out like base captures. but instead of standing in the designated area, you simply shoot at the boss.

That way the "tension/risk/excitement from the encounter" remains without a team feeling cheated.