He softens when she apologizes, and also gets a bit sad at being reminded of that. He had been pretty worried and upset at her disappearing, even if he didn't really blame her for it.

"It's okay," he answers softly, and he does mean it. "You'll get to eventually, and then it will probably be a better time for it."

You know, sometime when they're not all worried, and Ted is on pain meds, and he hasn't had a chance to tell Michelle about Joan. It would have been nice, but it also would have been a bit awkward.