Update: It seems my problem was not resolved quite so easily.
All three sites then proceeded to crash despite having their plugin files and MU php files removed.
I tried to upload the latest plugin files again via ftp to see if it would allow deactivation but the sites still crashed.
I then deleted those files but accidentally left the empty ‘plugin organizer’ directory in my plugins folder.
The site then loaded fine (!). I deleted that empty directory and everything seems okay. I also repeated the process with the other two sites using an empty ‘plugin organizer’ directory and they too now work fine.
I’m not sure I understand why this works? Does WordPress automatically deactivate a plugin with no files in its directory?
Anyway I’m back up and running. I hope this is useful to someone in the same position rather than just confusing. Perhaps it will be both!