I was having this issue as well. I tried lowering my weapons power to minimum and killing him slowly and that allowed me to kill him and the mission completed as it should.
This annoyed me a little bit as well. Though I can understand why, as it's an issue of how kits currently function. I'd like to see some Romulan specific kits available as an alternative to using KDF or FED kits, as that's already the case with ship availability for Romulans.
I agree with you on the default head bars, they are also often in the way when you try and rotate your character, your mouse will end up over one of the default heads so you can't see your actual head. And for gods sake where are the Undo/Redo buttons?