Okay first of all he didn’t R him he even said he could’ve taken the inhibitor but decided not to because he wanted to have the chance to do it with him
He didn't rape him. Alpha was utterly aware of what's happening and gave his consent. The only bad thing here was the omega running away because of his issues and keeping the kid from alpha when they meet again.
so he used his feelings for him and R word him while he was in a rut and then refusing to tell him he's the father...... right.