I say use the comma. I do ... just put it in a sentence. "Dear" acts as an adjective ... "Hello" is like a sentence, a greeting to the person you are writing to, and in English, we put a comma to denote the person being spoken to. Right?
Dear (adjective) John (subject),
Hello (greeting/senence/thought), John (subject being spoken to),
In standard prose, you would write, "Dear John, I have been waiting to hear from you." Or "Hello, John, I have been waiting to hear from you."
We only put the salutation up top in a letter to help the reader ... but it is still apart of the first sentence. Please correct me if I am wrong, but it makes sense to me! :)