The final battle in OOtP also seemed to scream Tom/Albus, with Albus saying (paraphrase) "You shouldn't have been here tonight" and telling him that the Aurors will be on their way. Not to mention Albus only shows up at the opportune moment when Voldemort finally makes an appearance. That he looks "almost frightened" when it appears that Voldemort might have been suffocated. I'm almost wondering if Harry hasn't picked up on this relationship as well.

You know, I half suspect Tom's anti-muggle stance might have been purely to be a slap in the face to Dumbledore.

I suspect too that everything went downhill once Tom left Hogwarts. Perhaps before he did, Albus realized he was starting to have severe anti-muggle sentiments, maybe even trying to reason with him.