Not that I can tell. My guess is that 'deleting' a comment actually sets a 'deleted' flag somewhere in the data base rather than actually removing it; but I haven't looked at the code so I'm just speculating.
> Is the idea of negatively voting down a comment ... To encourage the user to delete it?
No. The purpose is to encourage commentary that follows the site's discussion guidelines:
A nice feature would be, "negative points because". So that I can learn from it. I have a sneaky feeling it will be related to my opening line.
Im guessing im probably not the first to ask for that feature.