I was just reminded about this site, and this is a horrendously late answer to this question, but it's a good question and comes up often.
The advice that stuck with me was from my time at TNA, UK, and the most simple approach is to re-save your file as a simple image format and redact the information with black rectangles in the image editor. You'd then re-save the file without layers, so BMP is a good file format for this. I am reasonably sure JPEG would be just fine as well.
You could then recreate a PDF in acrobat with the new images if need be.
The National Archives UK have a redaction toolkit which goes into far more detail and may be of interest to the upvoters of this post.