Yes, こって is a corrupted form of ことで. It's rarely used in reality, and it usually has a scornful overtone in fiction, like in this scene.
This ご苦労なこって may look like an appreciation, but it actually is a sarcasm. It's like "What a (pointless) effort" or "You're working hard for nothing". Zoro is saying Luffy is putting effort to something meaningless.
EDIT: Here are other typical examples of こって:
Ha, [you] are so easygoing (though you shouldn't be).
[He] seems so happy (though it's not enviable).
This type of こって is interchangeable with こった (modal-ta).