I believe this has been the behavior going back at least to JBoss AS 7. I'm not sure about AS 6.
Can you provide more information about how this causes problems? If an mbean depends upon another I wouldn't expect it be possible to call it once the process of stopping it begins.
Is it a case of A depends on B, and then B wants to stop, but A must stop first (due to the dependency) and then when stop is called on A it fails because B is already unregistered?
Best regards,
Brian