Something just occurred to me: what about if, when we migrate to the new software, we have the "upload files" link be an option that is by default off...
I can certainly see removing it from the sidebar, since it can be accessed through "special pages" anyway, and sidebar space is at a premium. But I don't think it will be too much of a problem to still allow anyone to use it when (1) it should no longer be indexed by robots and (2) it will be a lot easier to clean up.
The only objection I can see is from regular "good" uploaders who will have to go through an extra step to get there. I don't want to get too crazy with user options either. 0