Is there a compelling reason to track sites.php with version control?
We track it. You can have more than one entry in sites.php that points to the same site, so we have one for the production site and then a few more for development purposes.

The file is not sensitive itself, because if you give someone the ability to read the contents of .php files on your webserver, then you have bigger problems! I'd say try and find reasons NOT to keep it under version control.

I have to say Gisle's suggestion of manually logging changes to files seems to be a bit more effort than I'd normally want to put in, to get round a problem that's not really a problem for me to begin with!