I asked about this in the SCP Discord channel and the consensus was that this was something perfect for scripting.
Now that multi-lock is in nightlies, I want to make a multi-lock missile that can only target a specific IFF type. So the player has Hostile1, Friendly, Hostile2 all in the view cone and targeting starts locking up only the Hostile2 ships even though both Hostile1 and Hostile2 are valid enemy targets.
EDIT: Nevermind, disregard! I just noticed you can specify valid ship classes for missiles now.. so I'll just use that!