You are 100% right; he wouldn't add exceptions for paid plugins into his free clans plugin because that doesn't make sense., and adding specific exceptions for each arena, or clans plugin etc wouldn't help either.
What needs to be added though, is a way for external plugins to force friendly-fire to a specific value. This could be achieved via a simple API call that would allow external plugins to force the value initially to true or false, and then a hook call when a player attempts to change their status.