Yes, the alternator housing is full of oil, as it should be.
You should probably replace all the case gaskets, alternator, clutch, oil pan etc.
If the engine was sitting for an extended period of time the clutch may indeed be stuck.
If may free up on its own after you run the engine a bit and circulate the hot oil or you may have to put the chain on it and rock the bike back and forth with it in gear while engaging the clutch to unstick the clutch.
If the clutch won't un stick you'll have to pull it and probably replace the plates.