That's the thing though, there is no "his harem" at ALL, and I say this as a fan of Kirito and someone that was very happy for the route Suguha took from her original route midway through Part 2 (As she's my second favorite character and I'm a big KiriSugu fan), is just 2 different girls taking complete advantage of him and gaslighting him for their own ends. Suguha at the very least DOES genuinely love him in her own very twisted way, but hilariously because of how awful literally everyone else is towards him in this game (Minus Klein and Agil), she still comes out on top as being the one doing the most for his wellbeing in the whole game. Sinon sees him as entertainment at best and a person of interest at worst, and she's already being targeted by someone else in the council of the Administrator Iluminati who wants her out of the way, so I wouldn't be hoping for a good ending for her either (If anything Fujino is just once again trying to create some forced relationship with Kirito because their canon relationship doesn't exist to enforce more the 'not-really-NTR' feeling when she gets screwed over by the plot). The one thing we gotta hope for is that her current partnership with Sugu doesn't causes her to be dragged down alongside Sinon when the other plot-device evil characters screw her over, really.
The point is, the entire reason those plots are allowed to exist is because they're basically being portrayed as BAD for Kirito, which realistically they are because they're just gonna hasten the dead of his 'relationship' with Asuna/make Asuna fall into Inoda's dick faster. Hell, you can't even count the Alice and Klein plot as anything GOOD for him, Klein just wants him to fuck Alice because he has been basically brainwashed into becoming a cuck and Alice into being a slut, Alice basically is now a whore that takes any and all dicks available to her for self-justified dumb reasons under the orders of her true 'master', even if she DID end up fucking Kirito it would just be a disappointing quick thing to hammer how much of a cuck Klein is and how much Kirito is being corrupted, then she would be going off to get fucked by 3 other dicks wherever her master wants her.
There IS a reason why the closest to a happy end regarding the main plot that has been CONFIRMED by Fujino himself is "Kirito doesn't know anything", because at least he will be in an ignorance is bliss situation of how screwed everything around him is. Ironically, again, the only one that can get SOMETHING resembling a true 'happy end' is Suguha, and only if she sticks with not actually revealing what she's doing to Kirito or if she guilt-trips him into sex, if she tries to do ANYTHING beyond that then the rules of Fujino's NTR-verse will kick in and screw her over :O