It's like you said, Magnussen only held Hamilton back by cheating. That's the thing that's different between him and Perez. Additionally, we've seen Magnussen do similarly cheating or grey-area things before when defending - it's kinda what he's known for. There's nothing wrong with playing as a team and ruining your own race and the guy behind you to let your teammate win, but you gotta stay within the rules.

And yeah, I agree that the penalty doesn't fix things for Hamilton but that can often be the case. I think it's too difficult to fix any other way though. Imagine there's a crash which retires the victim's car. You can't give them back their race so all you can do is penalise the other driver