Couldn't you just use a whitelist for the features?
If the reader can open a PDF/A-1 file and ignore the bad parts, can't it open a PDF file as PDF/A-1 and remove the bad parts, before saving it again?
Then you could use the "re-rendering" technique to extract images:
1. Create a stripped PDF/A-1 file from the original PDF.
2. In a VM, render the two PDF files to two high-resolution image sets.
3. Use some CV algorithm to find the differences. For example, gaussian blur, subtract, threshold, find islands.
4. Use this to come up with areas which use complicated PDF features and/or images. Say this returns that there is an image on page 9 in the rectangle ((17, 338), (400, 300)).
5. Crop out page 9 in rectangle ((17, 338), (400, 300)) from the original PDF. Use some CV algorithm to detect the DPI and whether it's best to encode as JPEG or PNG. Encode it and add to list of images.
6. Add sanitized images back from list, mark PDF/A-1 file with images as PDF/A-2.
Of course, you could do this for links or whatever as well. Spit out a list of rectangles and link targets in the PDF, and then put them back in.