There is opportunity to read between the lines here; this episode is the break-up episode.
Yes, the writers are hedging their bets and have Kes do it when she may or may not be controlled by an alien but their intentions are clear as demonstrated by the final scene in Tuvok's quarters as well as the fact that the relationship is over from this point on.
The scene with Neelix comes quickly after being "infected" and Kes mentions having headaches which I choose to interpret as a sign that she is still in control AND that her physiology is different to what Tieran has previously experienced. He later addresses the headaches as a unique phenomenon because Kes is a fighter.Kes: Everthing seems so different now. My thoughts and perceptions, even my relationships with my closest friends. You, the doctor, Neelix. How can I go back to my normal life as if nothing happened?
Tuvok: You cannot. This experience will force you to adapt. You are no longer the same person, and the course of your life will change as a result. Where that new course leads us up to you.
Plus there is a gap of "nearly two days" from taking them on board to arriving at Ilari where we don't see what has been occurring. I think there is clearly a case to be made that the transition is a slow process and not immediate. When they zap Janeway and escape, Kieran-Kes tells Nori to lock the doors "just like I showed you" but we (the audience) obviously never got to see this.TIERAN-KES: Do something about these headaches while you're at it. They make it difficult to concentrate.
ADIN: That's an entirely different problem. This body isn't accepting your neural pattern very easily. She wasn't a willing host like the others.
I take the initial headaches and the break-up speech as evidence that Tieran has yet to establish full control over Kes. Lien's performance here (which is excellent) clearly conveys that these are her thoughts and feelings. More importantly, the fact that their relationship is over "after" this episode strongly supports that view.
The passage of time during which viewers don't have the chance to see what is transpiring between Tieran and his confederates does leave an opening for interpretation and uncertainty. Though, again, from what we are allowed to see of their interactions, would seem to suggest the uncontested ascendancy of a shrewd, canny, and supremely confident operator like Tieran, playing out his designs, rather than a partial takeover in which both personalities are vying for control and are in conflict.
The scene that you cited some dialogue from between Tieran and Adin is interesting given some thought. Adin is conducting an examination to verify that the impact of the transfer is fully in place. It can leave open to question, why such a check wasn't done on board Voyager at Adin's earliest opportunity, is it an indication that such a test had been earlier done, perhaps with less than conclusive results, or might it be a simple follow-up check that Adin conducted with all of Tieran's hosts? Again, maybe an indication of the special nature of this transfer, as you suggest.
I do agree that the willingness and realization that a rupture with Neelix was what Kes truly desired, and that she didn't fight being led to the action, if she could've, by Tieran, as I believe was the case, also simply served to expedite the time when the decision would have been ultimately followed through on. Whether she had conviction to articulate it on her own at that time, it seems clear that it was, in fact, what she wanted, I think it is telling to notice that when the action is over, Kes seems to to not want to face Neelix directly and it's not him with whom she is meeting with back on Voyager, it's Tuvok.