Is it possible that Moriarty meant "IOU" not as a kind of retaliation, but that he felt he actually *owed* Sherlock?

Sherlock gave Moriarty a wonderful distraction, something he'd spent his whole life searching for. He didn't care about his criminal empire, the money, the power - all he wanted was a challenge, a game. He'd found a worthy adversary at last in Sherlock. Maybe he felt that he owed it to Sherlock, whom he took to be exactly like him, the same. He owed him one final game, one to top all others, that nothing would ever compare to again. They'd found their match in each other and, when all is said and done, he owed it to Sherlock to end the tedium of forever just "staaaaying alive".

As for Sherlock's mumbling "IOU" in the lab, I believe he was thinking more about what *he* owed than Moriarty's words at that point - punctuated by Molly's observation of him looking sad whenever John wasn't around to see. I believe he'd put together Moriarty's end game by that point and knew what was coming, what he'd have to do to keep the people he cared about, the people he "owed" for his humanity (aka the fact that he *wasn't* like Moriarty), safe.