Yes. And the Catholic Church persecuted Homosexuality, because anal sex spreads STDS much easier than vaginal sex. Disease was one of the major threats to Empires.
Also, there were always threats of invading barbarians coming in, and burning the whole of Europe, and raping women, killing children. The only way to combat this threat, was by having a large, well trained army.
Homosexuals didn't have offspring. Homosexual, and Anal sex didn't produce offspring. So, these acts were depriving Countries of soldiers, and thus increasing the chance that the country would be overthrown, and its people made slaves, or worse.
Everybody has a morale justification for what they do. The Catholics justified their persecution of the gays, because homosexuality caused undue suffering to the empire, by depriving it of soldiers, which opened themselves up to invasion by barbarians(which would cause TONS of people to suffer/die horrible deaths).
Why was Hitler able to become so popular in Germany? Was almost 50% of Germany full of "evil" people, who just wanted to commit Genocide? No. Hitler convinced the people that eliminating the jews would save the world from endless "undue suffering".
Even the KKK says they do what they do for the "greater good". They try to preserve each race's identity, and they value each race so much, that they think they should not be mixed, to preserve each race's identity.
What is the point to all of this? Everybody has a moral justification. Everybody thinks they are doing "good". The problem is, that nobody agrees on how to achieve that "goodness".
Even with this situation(slaughtering livestock), in this very thread, we have people who disagree with the idea that stunning is humane. Many people, in this very thread, are arguing that stunning is MORE painful, than a proper Kosher/Halal killing.
If everybody agreed that FORCING people to stun cows is more humane, or "good", than doing it other ways, then we COULD make a law forcing people to kill that way. But, if Everybody agreed, why bother making a law? I think we should just let people do what they think is "good". One man's idea of what is "good" is often different from the next.