If you changed the file to state=delete it should store the fact that file should not exist though - that would avoid this problem wouldn't it?

Granted you're trading in a bit of convenience for having state controlled in this way -everything would have to go through your config tool (ansible in this case) - I found commenting out tasks after I was happy they were complete in order to experiment with the next part of the config was a good way to make config changes like this painless and quick though.