I'm sure this would be possible if I added the villager data tag to the config myself, but it really requires some way of removing the instrument from them without having to kill them. Maybe adding this ability using Shift+rightclick?

Are you suggesting a disarm feature in general (definitely on my todo!) or is there a compatibility issue with MCA specifically?

Yes disarm feature is a good title for it! haha No, I have not noticed any compatibility issues so far. I just think it would be a cool feature to allow mca villagers play the instruments as well.