Well... Given that he thought "stop acting like you really love me", seems to me MC is still very hesitant to believe that... so your premise kinda doesn't hold ( ̄∇ ̄")
I could see how he has such reservation though, with the whole society being so unfriendly to omegas + the existence of an alpha in leadership being seriously threatening to his own status. I wouldn't have extra cognitive resources to care about romance if I were striving to establish my own footings in a male-dominant workplace too. Before any of my male coworkers happen to be my childhood sweetheart, they're first and foremost men that had everything so much easier than me. Not to mention if they could get in the way of my next promotion. And I'd loathe it if this sweetheart ever shows any sign that he conforms to the conventional gender roles ("women don't have to work so hard" etc).
Here, MC could've easily been blindsided by his prejudice/envy/distrust against alphas. And he'd be even more cautious/hesitant to acknowledge ML's feeling if he already has feelings for the alpha dumbass & is intrinsically insecure. We all feel smaller & more humble in front of our secret crush.
MC's been saying for decades "ALL alphas are the same, their 'love' just means 'wanting to FUCK,' so I never trust ANY of them," yet he decided to stay at the house of the very ALPHA who had tried to RAPE him just hours earlier (despite he noticed that the incident happened because that ALPHA had feelings for him), then that ALPHA trampled on his dignity and the sorrow of being an omega in the lowest way possible, completely disregarded it, drugged him, raped him, and even cum inside.
His brain is completely dead to the point that he even showed understanding and compromise for the rapist ALPHA's feelings to be genuine and for even commiting such a despicable crime, so why he never trust ML's words or feelings even for single second and has he been insulting ML for over 10 years, insisting that his obviously genuine affection is fake???
The conditions for becoming chairman that his father suggested is nothing but the issue just suddenly popped up recently.
There's no single room for fuckin' justification.

Yes MC Omega was stupid AF to put himself into that position with his alpha subordinate, but it's still not his fault he got raped. What's his fault is the way he's strung his childhood friend and fuck buddy alpha along on a string this whole time. He can't act like he doesn't know ML loves him, he just doesn't want his friend to "win" over him by being his alpha. Like I feel the MCs pain (as a woman myself) of wanting to gain merit on his own while being looked down on by men/alphas. But the answer to actually getting raped and the person you KNOW likes you gets mad and you say "not your business"? Fuck the MC I hope he suffers and chases the ML while realizing the position and power he wanted was worthless without him.