I'm 99% sure I know the answer to this one is "no," but--
Is there any way to make multi-targeting weapons hit allies when the allies are targeted? For example, if I set a unit with multi-targeting pulse phasers with a hitlocation set to 2 and use that unit to attack an ally, the pulse phaser blasts go flying off into space. I'd like it to be able to attack allies, but only when ordered to. When using hitlocation 0, the shots indiscriminately hit everything.
Uhm, why on earth would you want to hit your allied ships for? I don't know the answer, I'm just confused as to the point. But as you've got an "idea" as to how this may work, why don't you try that idea out?