I actually think the encounter with the Four Jedi Masters (from a Lightside perspective) was quite fulfilling. And not a surprise.
The people working on Obsidian seem to have an adoration for this theme - the hero who returns home only to be rejected by those she has saved. (Previously they have explored it in Fallout) The Jedi Masters are grateful to the Exile for saving them, but they still feel that she poses a great danger to what they love. And this is what Kreia's point is. This is the ultimate story of Knights of the Old Republic II - The Jedi Order is flawed. It has lost touch with true morality, and you see it in the response of the Jedi Masters when faced with something that they fear, that they do not understand. Instead of accepting their proper role, their stated role, they cast it off, and try to make the problem go away.
This is consistent with the true nature of the Jedi Order. It is this fear that is its cancer, and leads it to its slow drifting downfall during the rise of the Galactic Empire.
I think you see hints of this in the game. In Atton's backstory if you develop it, in what Kreia talks about, and in the musings of Master Kavar. The Jedi seem to suspect that there is something wrong, but it is Kreia who truly sees it. Kreia is just as twisted; she merely goes the other route and tries to destroy /everything./ If you follow G0-T0's conversation paths, though, you see that only two people have the right idea, WHETHER LIGHT OR DARK - the Exile and Revan.
So cheers to you, Obsidian, for having the guts to have the Jedi Masters play this role in this story. I think that it was /gutsy/ for them to have this story. I think that they haven't delivered a poor ending simply because they don't bash you over the head with it and show a medal put around the Exile's neck or a Sith fleet heading towards the Core. Yes, I agree that from a production standpoint it's a bit rushed, but there's /no/ weakness in the story. Or, more importantly, in the philosophy they have constructed.