Celebrim
Legend
Huh. I'm chagrined that my post might have come across that way.
As I understand it, the Yuan-Ti are a monstrous race descended from a group of demon-worshiping cannibals, who in a bargain with the Demon Lord Merrshaulk gave up their moral agency and free will in exchange for magical power. They ceased to be human and their flesh was corrupted and replaced with the flesh of demonic serpents. They now serve Merrshaulk as extensions of his will, furthering his quest to swallow the world and extinguish all light and life.
I'm a little mystified why fear and hatred of these beings would be confused with racism, as fear and hatred of demonic servitors is reasonable, where as racism is based on unreasonable fear and hatred of persons who are at a fundamental level no different than yourself and so deserve the same rights, dignities, and respect.
I am likewise a bit confused why you would suggest that the unjustified oppression of minorities is morally congruent with the problem of an actual alien demonic race infiltrating society. The Yuan-Ti do not appear to be 'misunderstood'. Indeed, it would appear to be a misunderstanding of the Yuan-Ti to suggest that they are misunderstood. There is no fashion in which a Yuan-Ti suggesting that fear and loathing of them be equated with racism is not deception, and likewise there is no fashion in which suggesting that racism be acquainted with fear and loathing of a demonic race is not demonization of real world other peoples. The problem of racism is not that some tiny percentage of oppressed peoples might possibly be something other than monsters, and so for the sake of the needle in the hay stack you ought to treat them well. The problem of racism is that the whole of a people subject to racial discrimination, whether personal or institutional, are in fact human.
The Yuan-Ti are not subjected to "negative stereotyping". Merrshaulk is not a nice guy who is just misunderstood. I suppose you could create a campaign world where all the lore about the Yuan-Ti is wrong, and everything in the monster manual is false, and then perhaps with some considerable reinvention you could tell a story about how these snake folk are unjustly persecuted and just misunderstood or maligned, but if you did that they would not in fact be "Yuan-Ti" any more.
But, if the lore about the Yuan-Ti is correct, then I really can think of no test that would prove an individual Yuan-Ti had moral agency and free will. Nothing that they could do in and of themselves could prove they weren't just soulless machines deceiving people to the ultimate ends of their dark master. I suspect it would require the intervention of an objective super-being to step in and say, "I vouch for this being. They are actually alive.", but in a world of illusion, could you even believe that it was a real Solar imparting such an incredible statement? And in a world of fantasy, wouldn't moral redemption be symbolically best associated with a restoration of humanity in the first place? Like I can believe, "I'm provably no longer a vampire, therefore I am not evil, so don't drive a stake through me now because I'm alive." It's a bit harder to buy, "I provably still have the flesh of a snake demon and therefore the bargain between myself and Marrshaulk is unbroken, but don't worry I'm actually good."
One little test here is why not people the whole world with Yuan-Ti, and then have humans be the oppressed minority that have to hide their existence? Why is it that when you think of something monstrously non-human, your first thought is to equate the monstrous inhumanity with minority groups? I don't actually think the alternate 'majority equals monster' story is any less racist if you cast that story in racial terms, but I bet I can guess your race by which group you want to make the monsters.