Basically ML & MC we're childhood sweethearts that got separated. ML is well to do (a prince?) while MC is from a herbalist family (?). ML leave behind MC with this memento. But when ML came back again to find the MC, he got a lot of people showing up with false claims. It didn't helped that MC had grown buff and tall and not like the cute self he was asking a child. So when ML finally met the MC, he mistakenly took him for a fraud and had him beaten up.
You guys forget the MC is this proud Omega who is struggling with the discrimination his secondary characteristic brings. And he projects that on everyone around him. On his father who doesn't clear MC's doubt that he prefers an alpha over his own Omega son. On his Alpha lover who doesn't clear MC's doubts about whether he really likes him or is after his position. And amidst all that doubt and anxiety, there's this Alpha subordinate who has left his family and standing to come and serve him. And who has never questioned his authority even as an Omega boss. Why would he not be a bit soft on that one guy in his life that never made him feel threatened because of his Omega status? That's why he returned back because he really trusts him. He knows how heats and ruts work and he believes that is something hard to control but can be explained. Unlike the behaviour of his father and the ML who aren't under any hormonal influence yet chose intentionally or unintentionally to hurt him with their word and decisions. I totally understand why he's chose to run to the secretary. It might be a mistake on his part. But I understand the emotional reasoning that led him there.