It also might simply cause people to work around the feature, by adding new top-level comments (that are actually replies to nested comments). I will be interested to see how well it works.
A. "I know this is sloppy and will be found out sooner or later, but I hope people will respect the restriction anyway."
B. "I know this is sloppy, but I hope nobody will find out."
C. "This isn't really sloppy, as I know full well the security implications and don't care about them at all."
D. Didn't really think about the implications.
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).