And this is why I do not ever tell someone that I have prayed for them unless I have good reason[*] to think that they will receive it in the spirit in which it was intended -- "I have set aside a fragment of time to think about you, even if there is nothing else I can do to help right now". I'm a Christian, but I can't stand the sort of "praying for you" that you describe, for exactly the same reasons you describe.
[* This generally requires them to have explicitly asked for same.]
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[* This generally requires them to have explicitly asked for same.]