Clean eating means eating as close to the natural state of a food as possible. So fresh tuna would be cleaner than canned, but I expect canned would be cleaner than the stuff in the pouches. And tuna in water is of course better than in oil, but you know that one already.
I'd say canned tuna is okay to incorporate into a clean eating diet. It's low fat and pretty healthy. And besides, we have to all make adjustments - canned tuna is incredibly convenient for those of us on the go!