Try this: After cropping in Preview, instead of saving directly, Print, then choose Save as PDF... under the PDF menu on the Print panel. This creates a new PDF with none of the original content. The extra steps are a pain, but you might be able to AppleScript it: save the PDFs as you're used to, and add steps at the beginning of your AppleScript to open up each file, print and save as PDF (if those actions are in the AS dictionary).
Try this: After cropping in Preview, instead of saving directly, Print, then choose Save as PDF... under the PDF menu on the Print panel. This creates a new PDF with none of the original content. The extra steps are a pain, but you might be able to AppleScript it: save the PDFs as you're used to, and add steps at the beginning of your AppleScript to open up each file, print and save as PDF (if those actions are in the AS dictionary).