But, I was able to compile the following and verify that libxml2 is able to clear the namespace, so the problem must lie in the XS land:

#include <stdio.h>
#include <libxml/tree.h>
#include <libxml/parser.h>
#include <libxml/xpath.h>
#include <libxml/xpathInternals.h>

int main (int argc, char **argv) {
  xmlInitParser();

  xmlDoc *document;
  document = xmlParseDoc("<r xmlns:p='http://p.p'><p:a>HERE</p:a></r>"
+);

  xmlXPathContext *xpc;
  xpc = xmlXPathNewContext(document);
  xmlXPathRegisterNs(xpc, "p", "http://p.p");

  xmlXPathObject *xp;
  xp = xmlXPathEvalExpression("/r/p:a", xpc);
  if (xp == NULL) return(1);

  xmlNodeSet *nodes;
  nodes = xp->nodesetval;

  xmlNode *node;
  node = nodes->nodeTab[0];

  xmlSetNs(node, NULL);

  xmlChar *s;
  int size;
  xmlDocDumpMemory(document, &s, &size);

  char *string;
  string = (char *)s;
  printf("%s", string);

  return(0);
}
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Outputs:

<?xml version="1.0"?>
<r xmlns:p="http://p.p"><a>HERE</a></r>
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($q=q:Sq=~/;[c](.)(.)/;chr(-||-|5+lengthSq)`"S|oS2"`map{chr |+ord
}map{substrSq`S_+|`|}3E|-|`7**2-3:)=~y+S|`+$1,++print+eval$q,q,a,
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