Agreed. Maybe I was too young to remember, but I don't recall any similar outrage over Superman throwing a totally harmless and depowered Zod to his oblivion in Superman II, or throwing a similarly depowered and harmless Nuclear Man to his death in a nuclear reactor in Superman IV. And remember that huge rock crushing Luthor's henchmen in Superman Returns? Guess what folks ... Superman caused that all by himself when he started to lift New Krypton.
What is it that's causing such controvery with the MOS ending ............. what he did, or the way he did it? A broken neck is certainly a bit more brutal and more graphic than the (off-screen or indirect) deaths in previous Superman films, but IMO that's what makes the ending of MOS so hard-hitting. There's a buildup and it ends violently, with emotion, and Superman having to do the one thing he obviously didn't want to have to do. I love how they did it.