The folks behind the InfoPath team blog have posted a short series on how to programmatically modify InfoPath form templates. The example in the series shows how to change the URL of a XML Web Service end point used by the InfoPath form using a script instead of having to do it manually by launching InfoPath. The posts in the series are linked below

1. Modifying InfoPath manifest.xsf file from script (1/5)
2. Modifying InfoPath manifest.xsf file from script (2/5)
3. Modifying InfoPath manifest.xsf file from script (3/5)
4. Modifying InfoPath manifest.xsf file from script (4/5)
5. Modifying InfoPath manifest.xsf file from script (5/5) 

The posts highlight that the InfoPath XSN format is really a CAB file, and the files that make up the template are XML files which can easily be modified programmatically.