running mongod --repair, without the same options as used via the rc.d script, isn't going to work.

Running repair therefore involves looking at the rc.d script to get the correct options. To make things easier the attached diff (against http://aur.archlinux.org/packages/mongodb/mongodb/mongodb.rc) adds repair as an option to the startup script. I didn't add removing the lock file as there is an open ticket to remove the lock file (or try to) as part of the repair process.