Dumbledore as an enemy made for a Rorschach moment on my end: "Dumbledore? Cannot imagine more dangerous opponent."
He's the greatest living wizard, by far (in canon he beat the holder of the Elder Wand in a duel). But it makes sense- I would not surprise me if Yudkowsky sees mysticism as the main problem, not mustache-twirling villains or greedy racists. And in chapter 17 Dumbledore admits far more than Harry thinks he admits.
But, Dumbledore has also done things to help Harry. The father's rock is a Chekov's gun- it has to be useful somehow at some point (probably Harry detransfigures it at some point to now have a large projectile he can hurt someone with). Whether this is just playing Harry / grooming him into doing what Dumbledore wants him to do or if he's genuinely benevolent remains to be seen.
I think a lot of it depends on how Yudkowsky deals with Harry being a horcrux. If he is one, it would make sense that a smarter Voldemort, on realizing what has happened, decides that he might as well build Harry up (since he's sort of forced to be on Harry's team now), and Dumbledore would eventually realize that Harry isn't going to be a nice little sleeper agent and finish off Voldemort, causing Dumbledore to take manners into his own hands. If he isn't one... then it's harder to see what sort of game Dumbledore is playing.
But a duel between Harry and Dumbledore (or Dumbledore and Voldemort) seems inappropriate. This is rationalist fiction, and in rationalist fiction you shouldn't win by punching the other guy harder. It seems far more likely that Harry and Dumbledore will get into another debate at some point.
That does make one wonder, though, what all the different players want.