I don't recall any ambiguity about that scene... having watched it recently, I remember the Doctor being quite confident about the conclusions he reached. I suppose it's open to interpretation, though.
The Doctor was like, "Eureka, this is what happened!" However, Janeway has a thoughtful look on her face. Also, there's no way that the locals could have known anything about what occurred or would have occurred. The book seemed to treat it similar to Janeway discovering how a magic trick worked and I didn't get that vibe at all.
Still, I had good vibes about the book from many locations. I just felt bad about losing so many good characters.