Dunno about online debate, but IRL, if it is clearly said with good intentions then getting annoyed about it is pathetic.
Getting annoyed at someone genuinely wishing you well simply because you would prefer them to have phrased it slightly differently is petty arrogance and a total **** move.
I'm not sure it's fair to depict that kind of reaction like that. To pray for someone is, implicitly, a bit different to simply wishing them well. It is to imply that a person
possesses some deficiency that needs healing or changing, often by simply being the person they are or having beliefs or opinions not in line with the "prayees".
I'm certain it can be said with the best intentions, but I believe those intentions are largely influenced by the culture around praying which tells people that prayer is selfless rather than the actual implications of the prater itself, or the subtext of telling someone they need to be prayed for.
I don't believe I've ever been told "I will pray for you" maliciously, but I still reserve to right to say to someone "Actually, I do find the fact that you've said that somewhat insulting and I'd rather you didn't", and I don't think it's a **** move. I don't say it to make them feel bad, I say it because it's the genuine affect to me of their words, and I want to increase their awareness of the implication of what they have said - even if they think they mean well by saying it.
There are exceptions to the above, of course, such as prayer following loss or tragedy, which more often is - as you described it - simply wishing well and hoping for healing. I'm talking explicitly about people who say it as a reaction to me being an atheist, or expressing a belief they feel makes prayer for me necessary.