- It's wrong because that is God's judgment and he is the source of moral value
- It's wrong because it's not natural
On the first point atheists as I see it can just make two comments
- We don't believe in God so if we believe in moral values, God isn't the source
- This renders the question "even if God judges that X is wrong, is it in fact wrong?" incoherent which seems at least odd
Iirc, Plato asked the second question in some form like "is the holy holy because God loves it, or does God love it because it is holy?". The important moral questions are just trivial confusions if we take the view that God (in his revelation) is the only source of moral value. We never need (or are able to) ask "is this a good thing to do?" we just look up what God has revealed. I submit, that in the particular case of Christianity (and to be fair here, I think most religions) this can have some pretty strange if not repugnant results (the Amalekite genocide comes to mind).
On the first point, since I'm a humanist, I believe that humans are the source of moral values and have to struggle to understand good and evil themselves. Even if I were able to believe, then I'd have to decide in just what version of religious morality I believed. This of course is not a fatal flaw in the religious position but it puts the burden on the believer to explain just why they choose the religious morality they do and from that point any perceived moral flaws in their religious creed become pertinent. For instance, taking the Christian scriptures at their word, they dictate execution for a rebellious child. Now, I think that's abhorrent, why do Christians believe it's justified - well I guess I've answered that - because it's God's judgment.
The second point seems to me to be more straightforwardly flawed: natural and unnatural are not moral categories. Plenty of unnatural things are morally neutral.