I don't think that's true in any important way.
I might say: "Killing Joe is bad because Joe would like not to be killed, and enjoys continuing to live. Also, Joe's friends would be sad if Joe died." This is not a sophisticated argument. If an atheist would have a hard time making it, it's only because one feels awkward making such an unsophisticated argument in a debate about morality.
This doesn't answer the question. Why is doing things Joe doesn't like, or making his friends sad, bad? Consequentialism isn't a moral system by itself; you need axioms or goals.
Link to Blog Post: "Extremism in Thought Experiments is No Vice"
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This is a LW discussion post for Yvain's blog posts at Slate Star Codex, as per tog's suggestion:
Scott/Yvain's permission to repost on LW was granted (from facebook):