Any way to get around this other than alt-deleting every single enemy to make sure I don't little miss muffet?

This is mission 7, the one where you have to get a data pod. I've never encountered this idiot problem in WC2 before (they just get mad at me for misfiring in the middle of a dogfight).

I couldn't quite get the generic wingman in that mission to go up on comms. In general for WC2 I found that I had to avoid telling them to return to base since it seemed to crash the game quite a bit.

Either way, I guess if I ever end up playing the game again I'll just alt-delete a lot. I just finished SO2. I'm hoping it's possible to transfer my save to 3?

You have to get her in your targetting sights to be able to bring her up on comms. Not sure about transferring the saves just yet, I've got about 6 missions left in SO2.