Well, I guess it can exert an oversized impression, out of proportion to the totality of what we had come to know (and for a good number of us love) about the character, simply by being the last and, by far, the most recently executed representation of her. However, for myself, I feel able to see it as a one off that doesn't in any way, materially impact how I view and value Kes. Personally, I don't find the premise implausibly out of hand and I'm rather dubious that the decision to do this kind of story, centered on her return, represented some animus on the part of TPTB. I just don't think I can find it credible to believe that an entire episode would be spent with the intent, explicitly conceived or even partially so, of pettily displaying contempt towards a small segment of the audience.
The idea may have simply been to revisit someone from the ship's past and would seem to suggest that at least some higher ups didn't, in fact, give the character short shrift in the backstory of the show, despite what I clearly feel was a stark and lamentable failure to recognize and highlight the spectacular talent that they had in their midst. In fact, not knowing the details for how the germ of the idea to bring Kes back came to be, as unlikely as it might seem, I wonder if it was generated or at least bolstered by someone's feeling of concern for the downward path that Lien may have already been seen as falling into, and the episode may have been an attempt to give her some exposure again, so as to help her get back in the game, as it were. That may very well be a conceit, fanciful in its likelihood and not supported by any real foundation, but I find it interesting to contemplate the possibility, even, of such a scenario.