Tsumugu has always been a sympathetic person (in actions, even if not in expressions) and was helping the sea folks well before he could have developed any special feelings. He would defend Chisaki even without a romantic interest. She was left all alone on the surface and has now been living for five years under Tsumugu and the geezer's care. There's no way he wouldn't treat her preciously just for that fact alone. He would have needed to hate her for that not to happen.
Well, I'm not saying he's not having an interest in her. I'm merely saying that it's still slightly possible he doesn't and far more possible he has but nothing at all will ever come out of it. After five years it's safe to say Tsumugu isn't overly likely to ever try to actively push Chisaki forward, perhaps due to being afraid that could sever whatever connection they now share.