Pad holes are filled in Eagle
Try using 'CAM Processor' instead of Print:

Choose 'PS' as output device and give an output file
uncheck 'Fill pads' in 'Style'
make sure only layers Top, Vias and Pads are selected (or Bottom, Vias and Pads for the other side)
click 'Process Job' and ignore the warning about layers not matching the layer setup.

Then you can print or convert the PS file to PDF.
I'm using an earlier version of Eagle (7.6.0), so things may be a bit different.