I don't know about that...there have been a lot of military cultures in the past that ostracized the disabled but welcomed homosexuality, or at least turned a blind eye to it (Greeks, I believe?). I'm not sure if the mentality behind Andalite ableism was so much 'it goes against society' as the fact that the Andalites are a hugely militaristic and form-focused culture. They pride themselves in their bodies and physical capabilities. I don't think we ever really see an indication of what their views on homosexuality are.
Nor do I think we can really extrapolate how they have sex based on their similarities to horses. I mean, they eat through their feet. For all we know, they don't breathe through their nose but through their eye stalks. Maybe they keep their sexual organs in their tails? Their physiology is so radically different than Earth animals already that who knows who knows.
Just my two cents because it's late and I'm babbly.