I also encountered the same problem on a large site. I forked the plugin on git-hub and asked you for a pull request.
https://github.com/short-pixel-optimizer/enable-media-replace/pull/99/commits/37cf6490a1e5e89dc191a8dc37f576454d475d07
I simply ask you to add an apply_filters, although in my opinion you could add an option so that the user can declare that he does not want any replace in the contents.
