Without hacking the plugin, it doesn't look like you can have the Extra fields above the default fields so you would have to use absolute positioning like you mention above. However if you do want to hack the plugin to do this it isn't hard. Just keep in mind if you upgrade the plugin your changes will be overwritten!
1) Navigate through to the si-contact-form plugin and open si-contact-form-display.php. Find where the Extra fields code starts, for me it was line 311.
2) Cut those 10 lines out.
3) Paste before the default forms get printed. For me this was line 163, you'll see a comment about checking for user's email address.