I think advice columnist Prudence over at Slate botches this particular Q&A:

Dear Prudie,
I have been an atheist for the last several years, ever since losing my (Christian) faith following a close friend's untimely death. Recently, my boss's mother told me about a serious and risky surgery that her other child would soon have. After I said to her, "I'll keep him in my thoughts," she responded, "Oh, would you please pray for him?" I said yes, and she began talking about her belief in the power of prayer, a belief I once would have shared. At the time, I wanted to comfort her in any way that I could, so I agreed with what she said. Also, it hardly would have been appropriate to launch into a "Why I'm an Atheist" speech. Later, though, I felt very uncomfortable with the fact that I'd lied and acted as if I shared her beliefs. Is this kind of thing a no-win situation?

—Not a Believer

Dear Not,
Maybe when you said you would keep your boss's brother in your thoughts, you were telling a white lie because you didn't intend to really think about him again. I agree, people should not be shanghaied into professing beliefs they don't have, and there are times that if you feel pressured to do so, you simply have to say, "I'm sorry I don't share your point of view." Additionally, when someone says they'll keep an ailing person in their thoughts, instead of their prayers, it should be a tip-off that they don't do prayers. But in this case, by going along you've simply tried to console a woman in distress. You're right: If you had responded to her request with, "I'm sorry, but I don't pray," she would have felt worse, and by causing unnecessary awkwardness, so would you.

—Prudie

The first sentence of her response is just offensive. She basically says that the writer was just flat-out lying about keeping the sick person in his/her thoughts. Nice, Prudence.

Then she says there are situations where it would be acceptable to say that you don't share a religious point-of-view, but that this wasn't one of them. Which situations are those, I wonder? Ones where you're not going to make the other person upset?

Yes, the woman was distressed. She's looking for comfort and she deserves compassion. But she wasn't satisfied with the writer's initial response ("I'll keep him in my thoughts"). She pressed for more, and at that point, not only is there nothing wrong with the writer stating her beliefs, it's an imperative.

In tiny interactions like these, majority belief systems are able to continue to marginalize people who think and believe differently. By pretending to be a Christian when you're not, you're reinforcing the presumption that being an atheist is aberrant.

If someone in pain asks for compassion, you should give it. Offers of sympathy, support, and assistance are all appropriate. But when they cross the line to lumping you in with their belief system, politely reiterating your offer should be enough. If pressed, you should then let her know that not everyone in the world believes the same things she does. If nobody ever did this, then minority belief systems would forever remain in the shadows, continually marginalized.