This was changed in core in MDL-48227 and to change the location of the message you would need to modify code I'm afraid. We made the change because many email clients (mobile in particular) were showing the "--If replying..." text as the preview of the message, thus making the preview particularly useless.
At around the same time, Ankit also designed a new way of adding this kind of information to outbound messages. Sadly this is master-only, but it may be of interest to you for 2.9. You can see it in action at https://github.com/moodle/moodle/blob/master/mod/forum/lib.php#L789
When 2.9 comes out, you will be able to move the text from the footer to the header by changing that 'footer' key to read 'header'.
If you feel it worthwhile to add the ability to swap them at will, perhaps you could add an issue to the tracker?