Instead of sending the XSN file you should send an InfoPath XML file generated by the server and the server can inject the sequence number before sending. Since the XML file already will have a reference to the proper XSN deployed on yoru intranet it will just open correctly.
If you must send the XSN in the email as your deployment method, you can always crack open the XSN on the server, inject the correct number in the template.xml, repackage the XSN and send that. The XSN is just a CAB file with a .XSN extension. There are readily available CAB tools available you can use.
Shiraz Cupala / Microsoft InfoPath MVPQdabra® Software / Streamline data gathering to turn process into knowledge