What is the purpose of thanking someone? To show your gratefulness of them, to show you appreciate them, and to show that you hold them in high esteem.
When someone else has updated their views, I do not feel grateful to them. The feeling of being condescending comes from that lack of gratefulness. However, I do hold them in either higher esteem and appreciate that people like them exist in the world. Saying so without the connotations of gratefulness sounds more sincere and appropriate.
"I appreciate that you took the effort to listen and update your beliefs. That is a hard thing to do, and I admire you for your ability to do so."
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?