We've always been a very laissez-faire group of moderators, and this has always been a fairly free board with a few notable lapses and exceptions to that policy, none of which I have personally supported in full.
So, in that vein, I would just say that if you don't like reputation, just ignore it. I enjoy it. It's an easy way for me to tell someone I appreciated their post without going through all the clicking necessary to send a PM. And it can be entertaining if you take it lightly.
I understand that it has been abused in some cases and over-emphasized in many cases... but I think that will diminish as the new wears off. Besides, some of the spazzing and squabbling gives the board character.
As of yet, rep-related arguments and sniping have hijacked less threads than I can count on one hand, so it's no biggie. If rep-related sniping gets out of hand at any given time in the future and starts to bleed into threads, let me know and I'll simply moderate the affected threads to keep them on topic and enjoyable.