Okay, I just went back to the anime, and reviewed the exact segment being refered to here.
Source? Funimation stream.
Episode 18 (Ep 6 season 2)
Time stamp: 12:18-12:40
The segment here, covers a MONTAGE of memories from Louis' mind. We see him groping her, fondling her, tieing her up, etc. We also see a 'doggy position' where he is looking over her from the back end, however, at no time do we see HIM CLOSE ENOUGH for him to do what is being reasoned above.
Rape his sister.
Was he close? Sure, I'll go along with that. Did he? Unless something official comes in the story or from the mangaka, It's reasonable to believe that he never crossed that line.
At the end of the segment, we see him in a chapel, bemoaning why she had to be born as his sister, and Holly is spying on him from behind a door.
The only real scene that has any apparent 'sex' in it is the scene with Louis and Holly.