> I think libxml does not have that problem
I don't know about that. libxml certainly doesn't round-trip XML documents in general (though I don't think it breaks namespaces at least), whether that breaks SAML or not I have no idea.
Anyway from tptacek's other comments it looks like general-purpose XML libraries should not be assumed suitable for SAML, instead they should have purpose-built implementation for the SAML bit, then once the document has been properly validated and the SAML bits stripped off I guess that can be passed onto a general-purpose library:
> SAML libraries should include purpose-built, locked-down, SAML-only XMLDSIGs, and those XMLDSIGs should include purpose-built, stripped-down XMLs.