Even if that idea is true, the prophecy provides the volition these reincarnations need to even go about the removal/destruction of the Tribunal. They wouldn't just do it for no reason.
True. But that's not the primary role of the Nerevarine, according to the prophecy. True, it might be an ulterior motive, but I would contend that the Nerevarine's purpose was also directed toward saving Vvardenfell from Dagoth Ur and the Blight. However, that meant destroying the root of the whole mess: Lorkhan's Heart. After the Tribunal lost the tools, there really wasn't that much alternative. I mean, look, the Tribunal didn't even keep trying to go after the Tools again to destroy Ur. Why? Surely the three of them had enough combined power to kick Ur's butt. Or, did the Tribunal
want Ur there, to make them look even more heroic and godly and needed?
EDIT: wait, now I remember. Ur had bound himself the heart and the Tribunal loved their power too much to make the ultimate sacrifice and destroy the heart (and their power). They were selfish, and when the Nerevarine came and made the choice for them, Vivec/Alma were resentful (not sure about Sotha Sil). Really, no one is in the right, and only Azura's meddling wiped the slate clean (be it an intended or unintended consequence of the prophecy and her scheme).