I wonder how Gene will react when he finds out that her mother has had sex with other boys
That depends on whether Gene is Wanda's son or not. If you play Gene as Wanda's son, there's literally nothing he can do about it except publicly embarrass his mother. He can't fight for her - with what, he's her SON! Wanda can always put him in his place: She can always say “You're not my husband or my lover, you're my son!”.
Gene can only withdraw and accept it.
As much as I would like to see that kind of drama and resolution in the VN, I think PopToc just isn't a good enough writer to write something like that. Just like another developer that keeps getting used as a comparison here (Sam vs Dylan).
So no, in my opinion it's not a good idea from a narrative point of view that Gene finds out his mother is having sex with other boys his age when he desires herself.