The problem remain the same as always. There is no reason to blame programs, what is to blame is how people use them.
Server Watcher and some other programs have been extensively used to harass targeted players in the past, one of the most notable cases was Doj and SMI. SMI could not log for two minutes before Doj would show up and kill him with ships placed all over sirius to ensure minimal travel time. It has by far not been the sole case of similar behavior.
So really, you're free to make whatever you want. Just be mindful of whom you give such tools.