One way of producing a culture some would find repugnant at first glance, but that may not be prone to the Evil Fantasy Culture stereotype, is to make some aspect of their lives repugnant to your players at first glance, but that is not something that they'd find morally or ethically wrong. This might help set up an expectation that they enjoy doing things the players WOULD find wrong, but it doesn't actually go so far as to make it a definite connection. In the case of real-world reptilians, almost all are hunters or scavengers, and a lot of people are squeamish about the way the real ones eat their prey whole or well... scavenge it... so there's some room for the fantasy equivalent to be unsettling without being directly Evil. This will need some balance elsewhere in the form of something the players will find particularly admirable; otherwise the PCs may just go off on a witch hunt, regardless, particularly if they're used to seeing the underground-dwellers solely as Evil Fantasy Races.
Also, if they've suffered a plague that many have high natural Con, it also follows that after this plague, the reptilians that survived were the ones that tended to be able to eat things that weren't entirely healthy when they died. This could be one reason they'd be scavengers; after the plague, most of what they could eat was plague-ridden, so they developed near-immunity to diseases and poisons in the food they ate. So while their negative happened in the distant past, there are definite clues to what happened to them as a culture. This could also be why they might be the artisans of another's idea: they revere their food supply, having nearly lost it, so their art is partly religious in nature.
Mechanically, that story would indicate that giving the reptilians things like +2 or +4 to saves vs. poisons and diseases wouldn't be a bad thing, overall. It wouldn't do much to raise their CR, though I supposes it MIGHT make it worth raising LAs, possibly, or in the cases of things like kobolds, at least make them suck less as compared to the standard races, so in the event that you let the PCs pick up one of the reptilians, if they're a little weak, it shores them up without being a significant combat power-up, and it's narrow range enough that it won't be an "always-useful" racial advantage, and instead would be somewhat situational.