I don't know the exact solution to your problem, but here are some thoughts.
Each XML form needs to be opened in order for the data query and rules to execute (and bring in the latest data from the secondary data source), then the form is resubmitted to overwrite the XML file in the form library.
Having the user open the form and resubmit is the issue you've run into.
So it seems as though what you'll want is some way of automatically having the server open and resubmit each XML in the form library, perhaps on a schedule (daily/hourly)? I haven't heard of such functionality, sadly.
I don't know whether a SharePoint workflow would allow updating the XML file in this way, but it's worth a Google search. This discussion seems to suggest it be done within the form itself.
Good luck!