I think enrollment keys is def the way to go as long as you tell the pupils (and staff!) about them. I'm doing the same here. It means they do all the work and you don't have to.I don't use the MIS tool as I've found uploading by csv perfectly adequate but you can upload users straight into groups in courses via csv if you want to http://docs.moodle.org/en/Upload_users#Upload_file_format
as long as you check http://docs.moodle.org/en/Upload_users#Updating_existing_accounts