I managed to get round it by having an entry stylesheet that reads the incoming document and the intended stylesheet.  It then modifies the intended stylesheet by adding the namespace nodes to the root xsl:stylesheet node and then used you extensions for compiling and calling the stylesheet.
  I know this relies on saxon but as that is my default xslt engine I have no problem.

From: saxon-help-bounces@lists.sourceforge.net [mailto:saxon-help-bounces@lists.sourceforge.net] On Behalf Of Michael Kay
Sent: 26 June 2008 07:59
To: 'Mailing list for the SAXON XSLT and XQuery processor'
Subject: Re: [saxon] Saxon:evaluate

Perhaps saxon:evaluate-node() will meet your requirements better? This takes the namespace bindings from the document in which the XPath expression is found.
If not, I'm afraid the answer is no - there is currently no way to set the namespace bindings.
Michael Kay

From: saxon-help-bounces@lists.sourceforge.net [mailto:saxon-help-bounces@lists.sourceforge.net] On Behalf Of martin.me.roberts@bt.com
Sent: 25 June 2008 16:09
To: saxon-help@lists.sourceforge.net
Subject: [saxon] Saxon:evaluate

  I am trying to use saxon:evaluate with an xpath that contains namespace prefixes that are not known to the base stylesheet.  Is there any way of adding the namespaces found in a document to the stylesheets context?