I spent the better part of a week attempting to create a PDF scrubber at my office for this same reason. We had become victim to highly targeted attacks from PDF sources. I wrote a scrubber in PHP using an open-source PDF parser
The project was shelved in favor of making users open all external PDF's on a virtual server that was hardened and re-imaged every evening to prevent any malicious code from running rampant. That's the simplest solution.