He has a reason for doing that. MC know ml is straight and Just the thought of "man who do man" is so repulsive for him. Mc not only afraid ml will hate him, but also afraid ml will be disgusted by the thought of them making love.
Actually it's been a long time i read the novel so i forgot if mc really know of ml's trauma or not
There is a lot more to it, ML has a disgust toward betas because of what his dad did to him so even though MC doesn't know what his dad did at this point he knows he doesn't like betas and would be disgusted to think he had sex with MC. Also MC thinks MLs family will take the baby away from him if they found out he was pregnant.

I think the bottom is trash. Making the person you love think they cheated and then not telling the them about “their” baby. Like wtf. It is not just your baby.