Instead of thanking someone, you could compliment them, or at least comment on how uncommonly reasonable they are. Someone once wrote this in response to me saying I was wrong:
... You know, I think we may be having a polite discussion, informed by reasonable data and fact-checking, and with considered re-consideration of claims and opinions, ON TEH INTERWEBS!!! ... I'm a little weirded out by this.
I didn't find it patronizing; I liked the implied compliment that I was unusually polite and reasonable.
Would it be supercilious to thank someone for updating? I know I would feel uncomfortable doing it, but I often feel the urge to do so anyway.
There seems to be something vicious about thanking them. My own estimation of my own belief has not changed in these situations. I feel fairly satisfied that the other has considered my view and has shakily come to agree with it. I worry it would be a little like saying 'screw your opinion, now you see I'm right.'
However:
It is both rational and polite to thank them. The gentlemen's agreement of rationality allows for one person to be wrong and not lose face at all. When someone concedes something to me (a point) I typically feel the need to thank them.
What do you think?