A quick Google searchs turns up the PDF Javascript Stripper, which appears to do just that.
But bear in mind that PDF is a subset of Postscript, which is a Turing-complete language. So there may be other attack vectors, not just embedded JavaScript (even if that arguably is the biggest one), and it’s thus mathematically impossible to know that your PDF is actually ‘safe’.
If a malicious PDF file targets a vulnerability in a specific PDF reader, or an associated library, then ‘sterilising’ them in a general way either won’t work (and thus give a false sense of security) or would be overzealous and remove too much information. Just imagine stripping all JPEGs from PDF files to avert the Microsoft GDI+ JPEG vulnerability…