I used Mp3Tag to remove the cover from all my files. Any tool that removes "Cover Art" from a MP3 will typically work to do so. You don't need a video editor to do it.
Yeah, I agree. Unfortunately isn't much we can do to easily remedy this though. Thankfully most of the newer EmuMovies uploads don't have this thumbnail embedded in them any longer. There are systems that still have a large amount of these though (which is less than ideal). I'll keep playing around and see if I can find a better way of working around them, but I doubt it will make it in with the full release.