I don't really think there needs to be a penalty; the incentive not to kill teammates is already quite strong (i.e. you want to win the match, and get more earnings for that.) I think it would be nice if it showed you team damage at the end of the match though. We know they track it, because they've used it as criteria for tournaments in the past. They just don't post it to the client for some reason.
I suspect that if players saw they did 200 team damage vs. 600 to opponents, they would modify their behavior on their own
ed: also yeah, a lot of the problem currently is the IFF bug. Even if you know about it, it's not always obvious which mechs are on your team if there's a lot of ECM flying around.
Edited by AssaultPig, 04 September 2014 - 02:41 PM.