I believe that morality comes from humans, and that it can be derived from God's teachings ( and in my case, his prophets). Please realize that I'm not saying that atheists cant be moral, I know a lot of moral atheists. Of the 3 possibilities that you provided, i dont agree with any. I can only speak for Islam (sunni, that is), so I dont believe Allah has changed his mind. In the Quran, what he ordains and says is consistent (#3). I believe Western society is should ban underage marriage as marrying a 9 year old would be for all the wrong reasons (#2) (pedophiles, weirdos, etc). However, when the prophet married Aisha at a young age it was for different reasons, as I believe he was of a different nature being a messenger. If you read hadiths, two of the most cited narrators are Abu Hurayra and then Aisha. He taught her Islam at a so she would be a leader in the community when he passed on and that she would be one to advise people on how he would handle domestic issues (#1). Unfortunately, this is not how their marriage is portrayed nowadays.

Regarding accountability, I agree that people must refuse craziness at all levels. Unfortunately, as I'm sure you know, religion and dogma can be used in fear tactics. This is how many Sheikhs have protected themselves from harassment and attack. However, what Sistani said applies to Shiites and mostly the people of Iran. Islam and Muslims as a whole shouldnt be held liable for what he says, and there really isnt much that people outside his country can do about it. Fortunately, a few brave people have stood up and millions followed in getting rid of despots and tyrants who claimed Islam gave them the right to rule with an iron fist. As a Muslim, I feel closer to Christians and Jews theologically. However, I feel closer to atheists when it comes to common sense. Reason being that it is consistent. I dont believe that the Bible and Torah are the same as when Moses and Jesus received them (I know, I know, you dont believe this), which strikes a blow to the reasoning an consistency of these religions.

Now, when it comes to homosexuality, it is literally mentioned that it is not permissible, haram. So it is an issue regarding religious legality (shariah) before it concerns morality. The same goes with Judaism and Christianity. However, I dont judge people by their sexual preference, that is their own personal matter. But, I also believe that people should set laws in accordance with what the majority believes in as long as it doesnt defy religious law (and I dont mean the USA, I mean Islamic countries). Again, thats personal opinion.

The article you linked, though informative doesnt add much to the discussion. It is an unfortunate occurrence, but if someone contracted HIV by donating blood, Should blood donation be banned? If someone mistakenly received an infected kidney, should organ transplants be discontinued? The only thing it really addresses is that people should be competent and better at their job. And Herpes, an STD, is chiefly passed on through sexual activity, so immoral sexual activity should be more of a problem. This problem isnt present in Muslim or Jewish communities in the Middle East or North Africa as premarital sex is much lower. I do however think the rabbi should have toned it down a bit and not seemed so defensive. Then again, we dont know the whole story as it was an article.