I play aliens most of the time, and I play Marauder/Adv Marauder. I get damaged by 'goon and tyrant FF regularly (well, tyrant if I'm stupid and get caugh in a tyrant scrum; I usually take damage from 'goons when they use their pounce attack to move around and I'm in a hunting pack with them). Any alien class that has a "button" attack, I think, can TK (dretches would be the only exception, since they just have a charge attack which doesn't require a button press). It's not as big a deal with aliens, though, because of regen.
In other words, if you aren't a tyrant, stay away from the tyrant rush. (Hell, even if you are you can still get TK'd; I joined in on a rush yesterday as a tyrant, and got TK'd while trying to get out of the scrum to heal up. No hard feelings, just statement of fact. It was tight quarters and plenty of stuff that needed attacking.)
As I said, regen nulls the effect of accidental FF hits for the most part, and getting TK'd is rare on alien side, and usually only during base rushes. Mirror damage would have little/no effect until a base rush, and then it could be devastating (since the general tactic is to run in, mess stuff up as long as you can soak damage and then fall back to heal, with the idea that you can get back up to full and rush again before the humans can repair and rebuild).
I'd favor the fine based solution above. I don't see the need to extend it to the aliens (admittedly, I'm a partisan), but I don't think it would ballance it much. However, the fine system has one downside: speed deconstructing. There is, unfortunately, one valid use of firepower vs own base, and that is to take out buildings _fast_ when doing a base move. I think this is a valid technique.
Jeff