I don't see how keeping Kes would have been any worse than keeping Harry. I mean, really, did he have any interesting character traits? Did he do anything significant over the course of the 7 seasons? Absolutely not. The problem with Kes - and many, many other characters in the VOY/ENT era - is that the writers never took the time to make them interesting, multi-faceted people. Janeway, the Doctor, B'Elanna and eventually Seven of Nine received a lot of character development. Chakotay, Tuvok, Harry, Tom, Kes and Neelix? Pretty underdeveloped, if you ask me.
The most interesting bits of Kes were were developing mental powers, and her Ocampan life cycle. If Kes had made it to the seventh season, there would have been the potential for some interesting stories about her impending death, and whether or not the crew would try to find a way to save her. There could have been some great drama involving the Doctor struggling to find a way to prolong her life because he doesn't want her to die.