The omega MC is upset with himself and actively abuses himself with medicine to ensure the safety of his alpha ML. Nothing untoward happens to ML before he ever reaches adulthood and everyone -ESPECIALLY THE MC HIMSELF - makes absolutely certain of that.That the MC's omega BODY still reacts to the alpha ML's presence is the tragic part, that they met far earlier than either of them were ever ready for - especially the alpha.
The whole point of the story is in the title. "Sayonara" is not just your standard "Goodbye, see you later". It's the kind of goodbye used for when you know you won't see the other person for a very very long time, to the point where you're unsure if you'll actually ever see each other again. MC and ML know that they're a fated pair, but they met far far too early to the point where they're uncertain if the bond is strong enough to make sure they could ever meet again, let alone still be with each other.
(Again, NOTHING HAPPENS WHILE THE ALPHA IS STILL UNDERAGED. The people bitching and moaning in the comments are people who didn't read the whole way through.)