It's a scenario he has tried to not think on. He knew well before Kal-El's birth that it was something that would never happen, that it was too late to ever have. He never expected to know his son at all, but here he has. It does not mean he will restrict himself to teaching only family, has not.

"To comfort you." He gives a smile in return. It's small, but readily present, and fully evident it's one. This had gone far better than he had hoped; while she may still have flinched earlier, he hadn't actually expected her to be willing to still continue learning from him, even in the case of her accepting the apology.