This. You can tell Johnny to F off. The game gives us an option to sympathize with him and I don't find that problematic either. I mean, after all you're a mad butcherer too. All those guards, gang members and whoever comes across your path die a violent death without a second thought. Ofc you can opt for a pacifist run but like 95% of playerbase will use those guns we're given.I mean I get your point and you do have an option to just shit on him every step of the story, give him no control and kill him in the end. You can totally express that he is no better than Arasaka in the story and pick a path that doesn't side with him.
Arasaka represents the dystopian element of cyberpunk and what Johnny did was to fight against that evil. Did his actions justify the result? That's up to you to decide. And I find that good, you can either embrace the "rebel against society" or side with the status quo and condemn his actions.
So no, I don't blame CDPR for making a morally questionable story. It could be, if we would be on rails against Arasaka and would have to cheer for nuclear devastation. But we don't. It's just history that happened and we can decide how we feel about that.