The problem is that even though you have FF7Music, theres nothing telling the original MIDIs not to play, so of course they do. Not hard to fix though, and can be done any of a few ways.
First and easiest, and the one I use myself, is go to FF7 Configuration, and to the Music section. Look for a device for playing the MIDIs that doesnt actually play them. I have mine set to an External MIDI device, which claims to be playing the music when tested, but doesnt actually play them through the speakers, or anywhere that Ive found. That will mean that in-game it cant play the music either, and therefore no more MIDIs.
The second way is simpler, just a bit of a pain if anything else on your computer uses MIDI. Simply go to the Volume Control, and mute the MIDI balance.
Problem solved, or at least it should be...