I've heard this argument before, and I think it's kind of a lame defense. The Donner films were enormously popular and shaped many people's image of Superman, even non-comic book readers. You can't just tell people to forget about everything they've ever known about the most famous superhero on the planet, just so you can screw around with the mythos to your liking. And if you ARE going to do that, your film had better be the most awe-inspiring masterpiece anyone has ever seen...which MOS, from what I've heard (it's on my watch list), very much wasn't. Even the people who liked it seem to stop at "It was better than Superman Returns", which is a pretty low bar.
There is literally no way, at this point in time, for a Superman movie to "stand on its own".
And just for the heck of it:
1. Just because something "happened in the comics" a few times doesn't automatically make it canon, or obligate you to put it on screen. Otherwise, why the hell isn't Bat-Mite in the Dark Knight movies?
2. Doomsday? Really?! That's probably the worst comparison you could have come up with.