The game PERMANENTLY taints your save file locking you away from the true golden ending if you do the Genocide run.
The game punishes you for playing the game. If they didn't want people to play Genocide, it shouldn't even be a thing.
Yes, the golden ending is corrupted afterward, but that's the point of the Genocide Run: to make you remember you pretty killed everyone just to see everything, the Genocide Run is a narratif tool and a commentary on 100% completionist, which is one the many tropes that Undertale play around with alongside SAVE, LV & EXP and others game elements, removing the Genocide Run would leave a black hole in the game themes, and if you don't like it, that's fine, but that's something that should be removed from Undertale (not to say every game need to have that of course).
Beside, yes, the best ending is corrupted, but if you play the game normally, you already saw what the best the game could offer, so what you would do after it? The Genocide Run is generally the last thing you will do, since Neutral Run can give you different experiences depending of your choices and nothing punish you to do before or after the golden ending. Undertale, despite all the foresight Toby put into it, is still a game after all, and no matter what you put into it, games become boring after awhile and you just move on. The pacifist/neutral run encourage to try the best the game as to offer and leave it once the player is happy, the Genocide run is in all, the utlimate run you will do if you want to try out the two hardest boss in the game and be done with the game, and as a final run, the events of it all make sad, but final ending for the game and the player.
Finally, is the punishment you get really that bad? It's not like the game is unplayable, you can play it just fine, and if you want a good ending, some neutral endings are bittersweet, but are still good to a certaint extend. I know it's a joke ending, but the Dog ending can be the note you can leave the game on, since everyone is happy somehow, or just do a really good neutral run, not everyone is 100% happy (then again, the supposed perfect ending isn't happy-happy for everyone either, *wink* goat bro *wink*, or for the snowman or mosnter kid if you are jerk to them), but the characters are still alright and hopeful for the future, so really, it's your choice in all.
And, if you don't care about cheating, you can also remove the file that corrupt the bad ending on PC.