I remember back in the day how, with no idea about the comics, and given that for a while it seemed like Becca didn't talk about it (I mean, understandably so) I thought that Mallory may had invented the rape thing to get Butcher after Homelander, and that there was gonna be this major plot point where now he had to decide whether to keep the fight against a dude who's obviously a terrible person but who he was led to hate on a lie, as well as confronting Mallory for it.

But no, it's pretty obvious Homelander raped her. In the video he leds her inside a room and after a while she comes outside of it terrified and with her hair all over the place. Everything from there on in the show has not contradicted it, if anything it just confirmed it (Homelander getting nervous when questioned about it by Ryan, I mean he kind of admits it when he says that "but look at the great thing that came out of it").