You know, having worked in a couple of writers rooms now, and having observed and at times participated in conversations regarding the direction of characters, story arcs, and what not, it is entirely acceptable to me that they got rid of Kes, and I can absolutely believe that the writers genuinely ran out of stories for her. This kind of thing happens. Stories have endings.
The other thing to consider is the high turnover rate of the Voyager writers over the years. The same way everyone was up in arms a few months ago about "Tattoo" being racist because they never quite figured out what nationality Chakotay belonged to, getting rid of Kes could easily have been the result of the same writing staff still being there after three years and just creatively burned out, it could be that Jeri Taylor herself was burned out, it could be that a bunch of new blood couldn't figure out what to do with the character.