Correct me if I'm wrong but I believe @dan and @ned are still working on a new reputation system. I think the solution to this should be built into it. Personally I believe reputation should be detached from the current upvotes and downvotes that steer it. I think I read that they are working on an algorithm that would include things like followers and resteems, but personally I think we need to have a little more control of reputation than that. Perhaps even a system similar to what we have for witnesses, where we actually vote on reputation alone, and can remove that vote in times where trust has been betrayed for example.
Just an idea, but for some time now people have been getting upset over silly flagging which wouldn't be such a big deal if it weren't for the effects on reputation.
Interesting thought. I'm not sure how many people would go to the trouble of a second step of reputation voting, but it could be a solution. Although we would see people campaigning for those votes and could further complicate the system for newbies. Thanks for sharing your thoughts.