Hi Jack, welcome to the forum!
Thankfully that's one issue I didn't have to deal with directly, I just had minor surface rust.
Without seeing any photos it's a bit tough to suggest exactly how to proceed. However, based on your description it sounds like your issue is occuring in the area shown being wiped off in this photo.
If you have "pretty significant rust holes" it sounds like a repair will definitely be required. It seems to me the right way to fix the area will be to pull off the door skin, cut out the corroded area and then weld in a patch panel. Pulling the door skin will be a pain but will likely make the repair work easier.
Depending on how many rust holes you have, and how big they are, I wonder if it would be possible to use something like a Dremel tool to cut out the corroded area and then weld in a patch panel using a series of spot welds to avoid overheating the fiberglass behind it. Once welded in place you'd then have to grind the welds smooth. This approach may save you some effort provided the deterioration isn't too extensive.
What do you think?