I think so.

Leaving around obsolete comments clutters the page, and these comments are no longer useful.

What might be a good practice, in case you're worried about the fact that "author's thanks is now dangling," you should [flag][1] that comment as "obsolete," because that comment no longer serves a purpose, either.

If you want to maintain a record of *why* certain edits were made, you can write that into the edit summary.

  [1]: http://meta.stackexchange.com/help/privileges/flag-posts