You need an editor that can apply transpose only to selected notes. (I guess automatic selection by instrument is not possible, and you have to select manually.)
Precisely what I am trying to avoid
I'm adding the functionality in to my instrument changer. I've got it working as long as some specific requirements are met first. I should be able to get it fully functioning with a little more effort. I am able to adjust the pitch via modification of the Note On and Note Off values present in the file, per instrument per channel. So if there is an organ on multiple channels, I can adjust the pitch of just the organ on a single channel, or on multiple channels.
It took a good bit of work to make it function, as the Game Maker Studio debugger seems to, once again, not want to debug my program. Plus it's been a while since I've worked on certain parts of the code and have to re-learn how I made some of it function in the first place. But I eventually figured out that my Note On tags were getting all incorrectly applied to a single instrument. Once I got that sorted, there was still chaos, as I forgot that the Note Off also includes pitch info, so after I would change the pitch, the Note Off was no longer "working", and the song would eventually descend in to complete and utter discord.
Now I have successfully modified three songs, hopefully with no ill effects. Further testing will tell.