I don't read him as worrying primarily about the immorality. As far as I remember his problem is more that atheism is amoral, if anything. The main concern is the lack of meaning. Humans crave rituals and spirituality. Now that we killed God we have nothing to turn to; how do we bury our dead now that God himself has died.

God is dead. God remains dead. And we have killed him. How shall we comfort ourselves, the murderers of all murderers? What was holiest and mightiest of all that the world has yet owned has bled to death under our knives: who will wipe this blood off us? What water is there for us to clean ourselves? What festivals of atonement, what sacred games shall we have to invent? Is not the greatness of this deed too great for us? Must we ourselves not become gods simply to appear worthy of it?

It's hardly one-sided when you consider what Nietzsche had to say about religion. Take Christianity:

Christianity was from the beginning, essentially and fundamentally, life's nausea and disgust with life, merely concealed behind, masked by, dressed up as, faith in "another" or "better" life.

Or more generally:

As soon as a religion comes to dominate it has as its opponents all those who would have been its first disciples.

His father was a pastor whereas he had a profound distaste for the church. Presenting him as a defender of religion is not accurate at all. I guess it's easy to misrepresent him because there are a lot of nuances going on, and his writings also don't always align perfectly.