Honestly I think the omega is crying, because all his life he had thought that he is an alpha and everything has changed so fast (he is an omega, he has a child) and he is afraid that he is nothing worth anymore, because he is an Omega He maybe is afraid that he has to rely on the alpha for the rest of his life. And in my opinion even though they both are bonded a no is a no.
But overall I still like the manga
Honestly I think, that even if Chanwoo would have left, MD would have gone after him. He is in love with Chanwoo and only wants to have revenge for Chanwoo rejecting him... that's kinda messed up (/TДT)/