jQuery Mobile doesn't do anything to disable file uploads. It just doesn't style them due to browser security restrictions and you can't upload files with the AJAX navigation system. I use file uploads with jQuery Mobile in my application with no problem at all.
If you want to use file uploads with jQuery Mobile you have to do two things:
1) Turn off Ajax navigation using data-ajax="false" on your form definition because you can't upload files using Ajax.
2) Specify the appropriate encoding type of enctype="multipart/form-data" on your form.