The scene has the same justification as the killing of enemies: To progress the game. "Here, go do this terrible thing that, for some reason, you find more terrible than the host of other terrible things you are doing in this game (one of which is arguably more terrible), or we won't let you get to level 6." Oh God this is disgusting ."BUT WAIT, we pulled the rug out from you. You actually didn't have to do it, that was a scene for a movie with actors acting."
And there's the kicker. For Hotline Miami 2, read: TWO, the only way to get that creepy uncomfortable feeling of Hotline Miami 1 back was to push the envelope. Already within the series people will have become desensitized to murder, even those who felt uncomfortable with the first game. Hell, read the article in the OP; the beginning of it is dedicated to how much they've expanded your arsenal and made it more detailed as if that's a good thing, and acceptable. But now every time you kill an enemy you're thinking about why that "implied rape which didn't even happen" scene was more uncomfortable than anything you've done so far.
Unless you just see Hotline Miami as an A to B mechanics experience which, unfortunately, a lot will because of the nature of the medium.