Well, there's tradition, and then there's persecution. I can see a good deity saying that family and children and fertility and reproduction are the most important thing, so gay people should marry the opposite sex and have kids even if their hearts aren't in it, because of the importance of keeping society going with lots of children and maintaining the family line. But I can't see a good deity allowing gay people to be imprisoned, or tortured, or burned at the stake, because of who they love. It's just not possible. I also can't see a good deity allowing this of nearly anyone, for that matter.
The Catholic Church had its Crusades and was still considered good by the standards of the times. Ditto for Islam and Judaism at several points of their respective history. Not to mention pretty much every country/nation/empire that has ever existed. Is that level of persecution "Good" with a capital G? Probably not. But if the society as a whole considers it a good thing, or at least a necessary thing, it's not likely a god like Moradin would have great reason to intervene. Going by the standards you list, no deity, country, or group of any size could ever be considered to have a good alignment. Which could be a fair enough statement, but one just as far off of the traditional D&D standard as keeping things as historical as possible.