As you guys have discovered, the restriction is in the code that generates the reply links, not the code that receives the replies. I'm hoping this will suffice.
It looks a little strange to have no replies on the comment at the bottom of the screen (especially given the 'link' feature).
Perhaps we could keep the 'link' exception, but just incorporate its use into the flagging algorithm (e.g. people who use it a lot get treated as if every comment they made has been flagged X times).