By all means, keep it anonymous. If flaming is a problem, then perhaps a report button for reputation a user has received? Then an admin could remove it.
Besides, taking away the anonymity would make people more hesitant to say something harsh. Maybe that's a good thing, but like ivo said, honesty. Of course, if it's overly harsh then that's where the report button idea could be useful, but I think the reputation system is all right as it is for the time being.
I mean, if people disagree then they should keep arguing and flaming in PMs.