Stabbing Gene in High on Life is just one of the many random impulsive moments that the game throws your way, but that's what it's all about. From the start you're thrown in at the deep end, gunning down random aliens and becoming a bounty hunter in space without too much second thought. Will your actions eventually catch up with you? Probably not.
After you've completed your first bounty job to hunt down 9-Torg and retrieve the talking knife, you'll arrive back at the house to find Gene surprised you're still alive. Knifey will ask you to stab Gene—since that's what Knifey does with everyone—and you'll have the choice to leave him alone, or to wander up and interact with him to deliver a stab.
If you're a more cautious player, despite the spirit of the game, you probably decided to look it up to check what the knock-on consequences would be. That said, here's whether you should stab Gene in High on Life, and what the consequences will be if you do.
What happens if you stab Gene?
In typical Rick and Morty style, High on Life isn't the sort of game that would make you take responsibility for your actions, and as such you can safely stab Gene. I say safely since, even though you stab him with the knife, he'll shrug it off and be back to normal the next minute, saying that he's survived worse.
Just as with choosing to kill 5-Torg, it doesn't seem like High on Life is going to blame you for doing impulsive, reckless stuff, since that's what the game is centred around. In fact, stabbing Gene actually gives you an achievement: Don't Knife the Hand That Feeds You. So, if you're a completionist, you'll need to knife poor Gene. Also make sure you stab Gene before leaving the house if you're going to, as you won't get another chance if you don't.