I'm opening this as a continuation of issue10761 since it was closed as fixed, and there's a bit more work to do there.

The fix for issue10761 was incomplete.  It did not handle the case where the symlink being overwritten did not resolve to another file (i.e. a "broken" link).  It also did not address the same issues with hard links.

The comments starting at http://bugs.python.org/issue10761#msg135924 detail the updates needed to complete this fix.