Quicktime doesn't seem to be messing with my PC. Perhaps you have yours configed differently then I do.  Mine doesn't try to play the every media file.  The only thing you have that runs in the background is a quickloader which is an option, its not even full quicktime just something to start it faster (which you can also turn off).  I also turn off  I use VLC to play most of my other media, quicktime to play .mov and also do some editing of somethings with it.

I do have mine check for updates, however you can turn that off.