Generally applicable to Superhero games, but I'm using ICONS as an example. I'm also going to assume that the heroes involved don't have reputations as killers: your minion has a different approach facing the Elongated Man than facing the Punisher.
So the heroes stumble into the bad guy's minions, and there's a fight. Maybe the heroes knock them all out, but maybe there's a point in the middle of the six minions to two heroes battle when two minions have already fallen, but the rest are still up.
It'll depend on circumstances, but why don't the minions flee?
I mean, sure, if each minion has the Quality "Fanatically Loyal to SKULL" then they fight to unconsciousness, but most minions aren't fanatically loyal...that's part of the reason they're minions. The villain went down to Thugs'R'Us and ordered a half-dozen, or something.
Do you have to fight until you defeat all the minions, every time?
Well, when I put it that way, no, of course not.
Again, circumstances: sometimes the minions have to go through the heroes to get out, so they're fighting instead of fleeing. But normally, why don't they try to run away after the battle turns against them?
Heck, why don't they try to flee as soon as the heroes show up? Maybe the villain has planned for it: "I want you four to steal the Illudium Q-36 Space Modulator, but if the Great Gang shows up, just cheese it. Make sure the Security Code Generator doesn't get caught—flush it down a toilet if you have to." Maybe not.
If you want a mechanical way to do it (and I don't recommend that, because it's just minion-on-minion action), roll Willpower against the number of heroes, with each additional minion being added like combining effort. If the minion succeeds, well, fear of the boss has won over good sense and the minion stays to fight. Minion qualities can add or subtract 2 to the roll.
Or roll your D6: A 1 is fleeing. As minions get taken down, that fleeing number gets higher. When 1 minion is taken down, the minion flees on a 1 or a 2. When 2 get taken down, the remaining minions flee on a 1, 2, or 3. When more get taken down, minions flee on a 1 through 4. At some point, the remaining minion just wants to leave or hide or surrender.
Your fled minion might be a source of future events. Maybe the minion gave the information to the boss, but maybe not. Maybe the minion hid until the boss was caught. Maybe the minion joined an opposing gang. Maybe the minion started a course, "Escaping from heroes," that's taught at the Annex (under a different name). Maybe the minion was scared straight. Or maybe the minion starts an anti-supers campaign against both heroes and villains because normal people shouldn't have to put up with such fear.