The basic premise of the game is that humanoids really are just funny-looking humans with token psychological issues to set them apart like in Star Trek
The basic premise of your game perhaps, but not of mine. And if you mean "the game" as if there was a single real way to approach D&D or Pathfinder, then you yourself are out of luck since it is you that wish to modify the basic assumptions. Since you have modified the premise and changed it, there is no reason to assert there exists some premise you or others have to adhere to. The basic premise of my game is that if you aren't playing a human, your basic outlook in particular areas is distinctly inhuman.
(otherwise their value system would be so alien you couldn't relate to them)
If you can imagine it, you can relate to it. It may not be emotionally provocative to you. It may not be attractive to you. It may even be distasteful, but you can relate to it.
Moral ambiguity only exists insofar as people have a choice to be good, evil or neutral.
Ambiguity certainly, but not morality itself. Only I think a Chaotic Neutral philosopher would assert that the act of choosing itself is the moral good, and not the choice made, and only a true Neutral one would assert that each alignment requires the contrast of its opposite to exist. But of course, this is an important sort of ambiguity in itself, as we have not answered the question, "Who is right?"
Regardless of whether a race is born and raised in evil (orcs, drow, etc) or even literally made of evil (fiends), they still have the chance to become non-evil and stay that way within D&D canon and vice versa.
Well, all I can say is that the D&D canon is ecumenical in its misuse of world religions. Fallen angels come to us by way of Catholic theology, under which construction all purely spiritual beings - whether angels fallen or unfallen - make eternal, irrevocable choices, based on their own fullest possible understanding and so stay as they are eternally. D&D has a tendency to at the same time claim both that outer planar beings are incarnated ideas made of the very stuff that 'good' or 'chaos' or 'evil' is made of, and that also they can choose to be other than what they are. But no one ever claimed that D&D's writers had ever thought particularly deeply about this alignment stuff. For my part, I like full palettes, so if I have something innately evil (say orcs or drow) that is capable of choosing good, then I feel I've already got my 'red' paint in several different shades, and feel the need for something that is innately evil and always will be (say a fiend of some sort). If everything is basically free willed funny looking humans with token psychological issues differing only by upbringing, then I feel like the only paint I have on my palette is gray and everything in my fantasy is going to look very drab and uninteresting.
My problem is that the Pathfinder books state categorically that drow and orcs and whatever are always evil and good individuals are generally killed young. There are no non-evil societies of these races anywhere in the material plane.
So?
I don't like that because it dehumanizes them...
Why is it necessary to humanize something alien? Is the fantasy world objectively better or the science fiction world objectively better if their are no truly alien things in it? Even if we assume that the real world has this feature, is it necessary and objectively better if the fantasy world is exactly congruent in every respect to the real one?
and turns them into nothing more than MMO mobs to be killed for loot
Well, to be perfectly frank and I think fair about the matter, most NPC's in D&D have historically only existed as things to kill and loot. The Monster Manual is just a big list of things and the loot that they have, and a dungeon is just a loot supermarket with potentially high prices but deep discounts if you do your shopping well.
whereas humans and halflings and whatever are free to be whatever alignment without being genocided.
Since when has that ever worked even for the real world? Being good or just doesn't make you immune to genocide, and arguably, if a truly good race were to ever encounter humanity, it probably would wonder whether or not such a vile scourge ought to be wiped out. In fact, a Lawful Evil philosopher would probably be quick to note that ultimately, the only possible good guys are the one that don't suffer genocide, and so ultimately the only test of whether or not you are good is whether you are doing the genocide or whether it is being done to you. It's better perhaps to assimilate, sure, but weighing the moral good of killing versus being killed, 'killing' comes out ahead in pretty much everyone estimation - and those that choose otherwise don't get their vote counted. From this, he reasons that the labels are just that, labels, and no one is better than anyone else, and his team is the strong, rational, clear headed team.
In a D&D world, this is a very hard argument to overcome, because what means do you have to overcome a boot to the face forever but might?
Anyway...
Moreover, I'd like to be able to play non-evil characters of those races without angsting about how everyone hates him and he has no place in the world.
Yeah, maybe I should stop replying as well.
Personally, I think that D&D errs in making races no more interesting than their stat adjustments, and most players do not play a race at all but a character sheet. Most players have no reason for playing races other than min-maxing, and evil races other than the superior stat blocks, powers, equipment and so forth that all date back to Gygaxian notions of D&D as challenging play (and the relatively limited tools he had available for that). That and a little 1990's still Grim Dark and "Silly Rabbit, Idealism Is for Kids!" thrown in.
I'm still waiting to hear what a non-evil human society would look like, so I tend to think maybe you have the problem backward.