So for point 1: I'd say let "no reputation" sites attract customers. If people want to participate in completely anonymous groups they are responsible for the groups they choose and the opinions in them. Good on them.
But for the rest of the people who lack the awareness, knowledge, or motivation to seek out these communities, we have a responsibility to find a way to make non-anonymous communication less toxic.
For point 2: Knowing the reputation of a user for the site you are visiting as well as their global reputation helps the reader make a more informed decision about the worth of this person's comments to them than without. Lets use politics. Assume a user with liberal tendencies argues intelligently with conservatives in Fox News comments where his comments are downvoted because they are diverging. They also comment thoughtfully on r/SandersForPresident where his views are appreciated and upvoted. When I see this persons comments on Fox, I will see his fox new's score is -128 and his overall score is 3. A troll on the other hand may have a -348 on Fox news and -828 overall. From this I can conclude conservatives don't like the first user, but some other people do like the first user. I can also conclude the second user is a troll, or doesn't ever participate in groups that share somewhat similar viewpoint. All of which you can see in their history, where their scores for various sites are listed, perhaps you could even bookmark scores for specific sites you want to see. Of course, this is binary, and can be improved with dimensionality, but is still better than nothing at all.
For point 3: Hell, what is someone hacks your bank account? I think a bigger concern would be someone automating downvoting of your account or upvoting of their own. Which would require more thought.