I've thought of another option: the Taunt!
The Taunt should be an action that you can't reasonably use in regular combat (some ideas on that in a moment), but causes such fear/frustration/silliness in the enemy crew that they abandon ship. The Taunt should be unavailable for the first 3-5 minutes or so of the match, and its cooldown should decrease with each successive use. Basically, it gives each ship a "personalized" (according to race) jibe at the other player - one more opportunity for entertainment and hilarity - which takes away some percentage of the opponent's crew. If a griefer tries to prolong the match I only have to suffer through it until my Taunt timer recycles, and maybe after 3 taunts or something I flat-out win.
As I said, obviously taunting should have some use restrictions. The first I mentioned is a taunt-use timer. Second should be a certain amount of time to emit the taunt, during which time the taunting ship is more vulnerable/can't fire weapons/slower movement - something along these lines. This prevents players from risking a taunt in a fair match where both are playing to win, but doesn't make it impossible. As such, taunting might become a risky but daring tactic for ships that are severely out-matched.
Now, the first obvious trouble I can think of is that if the taunt becomes available after a time, why don't both players use it on each other? And the griefer can always hope to get his off a moment sooner and actually win! My thought on this is that each ship has a built in Taunt Power stat, wherein the crew get more focused on the battle and less at distracting comms chatter the more they participate in the battle. Borrowing a bit from Hunam's idea or scoring aggressive actions, the more you've landed hits on me, or at least attempted to do so, the more quickly you build up a taunt, and the more protected you are from enemy taunts. This encourages a potential griefer to take an active role in battle or he will simply get taunted to death.
It also lends a small underdog tactic to lop-sided matchups. The Shofixti vs Ur-quan could mean my Shofixti ship could attempt a suicide run at the match start for maximum collateral damage, or it could mean I risk drawing out the dangerous battle to lay in with a taunt, but then I'm going to have to build Taunt Power to do so. If I think I'm the better pilot I could really embarrass my foe by staying alive long enough - all while darting in and out of combat - enough to find a safe few moments to taunt before self-destructing. But if I just run away my opponent will build up taunts more rapidly and I'll be sucking space before long.
In summary, this effectively means each match will have a definitive winner. It adds the fun possibility of extra ridicule to the game (it's Star Control - we all know we want it!). And most importantly it allows players to use tactics that are valid against the AI, while taking away (or at least limiting) the trollish fun of just annoying another human player.
Admittedly, I don't know what this would do in my previous Spathi vs Syreen matchup as the Spathi has a rear-firing weapon. But at least my opponent would have to fire once in awhile, and he'd likely hit me whether he wanted to or not, so the battle wouldn't continue forever in that scenario either.
NB: the taunt ability should be restrictive enough to use that it isn't a part of most combat situations, but it's there if you dare, and there if you need it.
Please proceed to tear apart my idea! Maybe we can make something better out of it - or maybe not 