Your response to the writer who submitted an article via certified mail was good, but missed the second part of the problem: submitting via e-mail. The editor asked the writer to submit the article via e-mail. Instead of jumping for joy and hitting send, the writer e-mailed back to point out the guidelines say not to submit via e-mail!
Writers need to know that the guidelines refer to initial contact, what we used to call “over the transom.” Once you have established that contact, if the editor asked you to send it via e-mail, for goodness’ sake, don’t argue about it!
This writer missed a possible sale by being too concerned with the letter of the law, rather than the spirit.