The same argument leads a rational person to stop obsessing about the supposed morality of killing humans. The touchy-feely appeal to "think about the suffering of the _humans_" is likewise species-ist
I think they're saying that you may have thrown out the baby with the bathwater. If your conclusion horrifies you—doesn't resemble what you were optimizing for—you may be optimizing for the wrong thing. Rationality isn't broken; revisit your optimization criteria. See the paperclip optimizer, the smiles optimizer, etc.