Game management is essential to the game. No one would like the end result of calling every single thing as written in the rule book. If you look back at any playoff game and retroactively assigned penalties, you'd be lucky to see 15 minutes of 5v5. The truth is, no manageable set of rules will, when called to the letter, lead to good hockey. It lacks the flexibility that a good game needs. The NHL and refs understand this, but fans don't seem to. This approach works better in far more structured games like baseball.
I've likened it to Godel's incompleteness theorems, except for hockey. Not a perfect analogy but it's pretty close. The game is just far too complex, with too many variations in play patterns, for a reasonable rule book to be able to be called mechanically like some seem to want.
Now that isn't to say that there aren't improvements to be made and that certain refs are anything other than complete trash. That missed call on Perry was pretty egregious. But the answer certainly isn't to call the rule book to the letter.
The problem isn't that everything needs to be called, it's that they let even the most egregious of offenses go.
You want to let a tiny little hook that didn't affect the play at all go? No problem. But when a guy is trying to drive to the net and he has a defender water skiing on him and it's still not called, that's suddenly a problem.
You want to let a guy get away with one single crosscheck in front of the net and give him a verbal warning of "do it a second time and you're gone"? No problem. When when a defenseman is allowed to take multiple crosschecks to the back of a player, follow it up by face washing when said player turns around to tell him off, and the ref STILL doesn't call him? That's an issue.
Do I want 15 PPs per game? No. But if a team is committing so many egregious fouls that it warrants 5 or 6 PPs in a game? Yes, call that. Don't let 4 of them go just so you can say you're "letting them play".
So no, it's not quite as black and white as you suggest in your first paragraph. It's not about "calling everything" instead. It's about calling the egregious ones, including the Perry high stick, while "managing" the game by giving the players a bit of leeway on plays that don't really affect a play in any tangible way.