VOY finale was a waste. Largely because half of the two parter is derivative of TNG's AGT, and the fact that the alternate future we spent so much time with was wiped out/will never exist thanks to Future Adm Janeway's meddling.
Well, that's only the case if one accepts that construct of the development and continuing existence of alternate timelines. As I perceive it, this situation like any other that might play out in the same manner, would leave Admiral Janeway's timeline thouroughly intact, with the only difference being that she would be permanently absent from it and you'd have one pissed off Klingon wannabe big shot raging around for awhile. Consider this, would Kim simply present his argument to Janeway, in person no less, as a case basically, of uncertainty about the outcome and the breaking of rules, if he knew his universe was about to be annihilated? Wouldn't he just come aboard the shuttle and stun Janeway, or if lacking that possibility, be forced to, without equivocation, to just destroy it? In fact, he even says that "If Starfleet Command finds out I had anything to do with this, they'll demote me back to Ensign." That hardly sounds like the concern of someone whose 24th century knowledge of temporal mechanics, tells him unreservedly that what you state as fact, is even the realm of possibility.
I would've preferred Voyager to wrap up unfinished business between the Kazon and the Ocampa; have Kes return to send Voyager back where it all started 70,000 light years to battle an eminent threat, possibly the female caretaker and the rogue Ocampas, where the Kazon and Ocampa join with Voyager; together to defeat the bad guys and finally make peace with the Kazons.
I've just very recently posted that a truly appropriate conclusion to the series, would be closing the circle, having Voyager's salvation come from Kes herself. You don't state it, but I'm assuming that following the action you describe, you would also have Kes send them back to the AQ. Perhaps not. In my estimation, there wouldn't be any need for Voyager to return to Ocampa. The scenario that you propose, just doesn't seem likely. Why would Suspiria and her acolytes return to Ocampa and threaten it, as seems to be the gist of your point? To prevent the development of any other natives that would develop the superior powers that Kes did to drive them off? No, it just doesn't seem to make sense. Also, at the same time, Suspiria seemed surprisingly impressed with Janeway's expression of mercy and forgiveness. I just don't see a reappearance of her to be presented as being a vengeful adversary as before. In fact, in the various possibilities that I've run through my mind as to how Kes would be brought back to make a final loving and perhaps dying gesture, one included Suspiria encountering Voyager in deadly straits against the Borg, and that she would be the instrument that would expedite having Kes become aware of the situation and be brought into the fulcrum of the action.
Unfortunately though, I don't think that any such resolution involving Kes or returning to the fate of the Ocampans, was likely ever considered. First, Kes had already performed such a feat to remove Voyager from imminent danger and to have such an occurrence happen again would probably be seen as simply unacceptably repetitive. More to the point, I really see that the final act that would serve as the ship's salvation, if that was indeed the intention, would have to integrally involve, if not depend on the program's signature character, the one who really provided the only significant degree of distinctiveness from what had come before in the franchise, and would need to be achieved against the series' signature antagonist. That it was conceived with the twist that was presented, was just an irresistible sweetener, I imagine, to TPTB. Anything less than this kind of denouement, would almost certainly have borne the risk of presenting a finale, that in their calculus I would think, had a great chance of being received as underwhelming, lackluster, and unworthy in one way or other to a great deal of the audience that had stuck around that long, just to see how things were going to be wrapped up.