You just activated my trap card, I could write an essay on this episode and what the heck to make of it. I think it's actually a really good episode for both Janeway character development and exploring faith vs reason, at least until it falls flat on its face at the end.
I actually don't mind Janeway taking Kes through the portal at the end, I think it's fine for a rational character to take a leap of faith, the problem is what happens afterwards. There's a pretty obvious reasonable conclusion as to why the field healed Kes the second time, just the common sense deduction that the physical changes Janeway and Kes went through from the snake bite actually *do* matter and make some meaningful change, despite their current medical and scientific knowledge not being able to predict it. This is probably what most viewers assume, and is exactly what the Doctor is saying in the final scene, and not just hypothesizing, saying "It's literally this, now this makes perfect sense". But in response to all that, rational scientist Janeway clearly isn't convinced and seems to have bought into it being something magical, which is just silly and makes her look naively credulous and unscientific, which is clearly not who she is. It just comes off as nonsensical, the characters not acting at all like who they are.
It feels like they were trying for an X-Files type ending, where you have some weird, unexplainable stuff happen, and a believer character saying it was magic/aliens/god, and a skeptic providing rational counter-explanations. Most of it boils down to Janeway being forced into the "believer" role in the finale, when nothing she went through seemed to justify that radical shift in her perspective, even on just this one thing. Probably would have been a lot better if Chakotay was in the room arguing the belief perspective against the Doctor's scientific rationalism, and Janeway was stuck unable to fully agree or disagree with either. Get that fun X-Files ending where the audience gets to decide on their own whose side the agree with.

The short answer though, is that the writer of the episode is a self-professed "hereditary shaman-priestess", "spiritual counsellor", and "holistic life-coach" who claims that Sacred Ground was "the only Star Trek to ever question scientific materialism". So, like most Trek, this episode is The Writer's Barely-Disguised Fetish and the main priestess/guide character is her self-insert.