I don't happen to think that killing someone who is good or killing someone who is evil are any less morally fraught for the person doing the killing. Unlike GM4Him, I don't see this question of alignment as an issue of escapism, though what I'm about to say might work towards it. It's more an issue of having a world that can have objective evil, with creatures 'evil' without choosing to be so, and one that makes evil a subjective concept, determinant to a character's experience. Creatures in D&D could be born of evil, and born evil, even if exceptional cases could act against their base nature, a base nature could exist, something that doesn't jibe with how people want to see alignment work, where nothing can be taken away from you through a choice you didn't make.
For instance, if I'm a neutral good peasant who through no fault of my own, trips and falls into a pit of infernal ichor. The changes that occur to my character aren't going to be just cosmetic. I might have grown horns, my skin might have turned red, etc. but more than that, being exposed to the infernal plane will effect me on a metaphysical level as well, my alignment might have changed too. Because alignment isn't just something we choose, though you can endeavor to change it. And just because my example uses the infernal plane, it can happen through any kind of magic, planar, divine, arcane. Creatures created through arcane experimentation (like the owlbear) can be inherently evil. There are still magical items in 5e that change your alignment.
I also don't think that intelligence is some kind of get out-of-jail-free card either, I don't think D&D has to operate on a level where, intelligent rational people are somehow better equipped to choose right from wrong.
For me alignment is most useful in a roleplaying game if it's kept totally hidden from the players. That quote from Mearls about choosing your alignment or letting alignment define you, isn't good roleplaying. Alignment should define NPCs and certain races, on a macro level, and there should be consequences for playing against an inherent alignment, but it doesn't sound like good roleplaying if the concept of alignment is what dictates your characters actions. You should be playing in a world the macro alignments have created. This is one of the cases for having alignment prerequisites when playing certain races, if you can't start out as a good Drow, you'll have to roleplay your way into a new alignment. People who want to play an evil race, should be forced to view the world from an evil perspective, and their transition into a new alignment shouldn't be a given.