Just because someone has power or is in charge doesn't mean that this person is right or is telling the truth.
Likewise, just because you think there were more stories for Kes to be written and told, it does not necessarily follow that those persons in charge of writing the show felt the same way.
The writers could have, easily, determined that there were in fact no more stories to be told and chose to write her out of the series and in their capacity as the showrunners and writers would still be absolutely right to do so.
As for "having the power" or "telling the truth," well to begin with, the showrunner is the king of the castle on a show. They're the voice, the head of the table and they make the big decisions. And for something like this, they'd likely have to sell it to the studio and network executives, so if you want to blame anyone, you better start blaming them as well.
Lastly, "telling the truth"? Seriously? Is this such a matter of import that even if the writers were lying (which I sincerely believe they weren't), we're going to sit around and point fingers?
Screw that. It's a goddamn TV show. Get some perspective.
The interesting thing is that the loss of the ability to write for Kes was very sudden. They were actually coming up with stories where Kes played an important part up to the last minute of her presence on board (I'm not counting "The Gift" since that one was a sad mess, written with the only purpose to get rid of the character as soon as possible, no matter how unrealistic the story was).
And only because someone has the power or is in charge, they are not above criticizm. In fact, it's our right as fans and supporters of the show to criticize what we think is wrong. After all, we did help to keep them in charge for seven years just by watching the show.