I normally agree, but in a finite storyline like this, I don't really see how having those characters alive but relegated to random cameos is more vital than telling a good story. If they didn't do the episode the way they did and played it safe, it would be pretty unremarkable and devoid of meaning. Even in the comics, it was so impersonal (and you knew Magneto wasn't gone) that it wasn't especially shocking or upsetting. You kinda went "Oh, damn" and moved on.
This episode has been huge and caused all these emotional reactions from people. Two of my friends, middle aged men, were weeping over the episode. It's the most talked about episode of the show. That wouldn't have happened if they hadn't taken those chances and had some fatalities. And I feel like it would be a disservice to the story and what it represents to have all of the characters we know magically survive this horrific massacre.