I think the mistake here may be to assume that your email was indeed as readable as you believe. Many times I've written a letter or email and felt the message was clear, only to re-read it at some later point and see that it could have been interpreted in a different way.
Regardless, the only resolution I could see being effective is a response along the lines of:
If you would read my email again, you will see that I said "{quote the misinterpreted part of the email}", therefore your response "{possibly quote the part of the reply which is misunderstood}" seems rather out of place.
The recipient only has two options at this point: a) acknowledge their error and concede the response was misguided, or b) clarify their different interpretation of your statement and why they feel their response is justified.
That seems about as tactful as you can be, whilst actually seeking to clarify the point.