I have not verified it, but there are about three possibilities to follow:
• flattening the document (using the flattenPages() JavaScript method)
• using PDFOptimizer
• applying an according Preflight profile
With the Preflight profiles, making the file PDF/A compatible should definitely get rid of the layers (but may have other implications later on, such as Acrobat not allowing modifications, unless you change some preferences).
Hope this can help.
Max Wyss.