After looking at the issue in more depth, the easiest way to use saxon9 for transformations is to save a copy of xslt.m (I called my new file xslt2p0.m) and then change line 146 from:
xformFactory = javaMethod('newInstance',...
'javax.xml.transform.TransformerFactory');
Change this code to point to net.sf.saxon.TransformerFactoryImpl. This should work at a minimum for instantiating new transformfactory objects.
xformFactory = javaObject('net.sf.saxon.TransformerFactoryImpl');