I agree that corruption should MOSTLY concern exposure to supernatural/otherworldy/Cthulhu-esque evil, monsters, demons, devils, etc.
I do see a point where corruption CAN be applied to a person for their actions. If corruption is only for "supernatural evil" then Adolf Hitler was as free and clear from corruption as a new born babe. I disagree with that premise (supernatural evil "only"). Same with Charles Manson or some of the "monsters" we humans have created. Some humans in our history have accumulated "corruption", "bad karma", whatever you want to call it from their ACTIONS. Every action? Not necessarily but I'm convinced Adolf Hitler was corrupt and he didn't come into contact with demons.
Some in-human/inhumane actions by humans should get corruption points. This in and of itself should be RARE but the GM should justly "reward" PC behavior- be it good OR bad. I'm not talking about a simple rape and pillage or killing. I'm talking about a PC who is consistently, deeply and without remorse engaging in acts of evil (which sounds like your pirate).
Conan wasn't a saint but I don't think he was corrupted. but then he didn't go around torturing everyone and anyone just for the hell of it from the second he left Cimmeria.
Reputation. Fate Points. Corruption. "Role-playing consequences" "in game". All are ways to deal with this. Let the GM decide but do remember, actions have consequences and PCs should man up and accept responsibility for whatever they have done/did.
My 2 cents.