I don't see it as going against someone's beliefs for me to pray for them. I wouldn't turn my nose up at the meditative thoughts of a Pagan hoping for my health. I wouldn't get mad if someone who was atheist didn't pray for me. To me that's respecting beliefs, respecting that each person is free to deal with life in their own manner, and respect that it does not have to mesh 100% with what you believe. But I suppose it's all a matter of perspective.
If someone doesn't wish to send prayers to someone, they can always offer to "send good vibes" their way. I have offered either of them to people who needed them. Sometimes knowing that other people care enough to think of you can help one more than they would think.