You could presumably put your own routine in place of magic_killbackrefs via XS; you'd need to do something like

int handle_killbackrefs(pTHX_ SV *sv, MAGIC *mg) {
   /* loop stolen from magic_killbackrefs, with
    * whatever you need to do to for each svp[i].
    */
   /* afterward, */
   return magic_killbackrefs(sv, mg);
}

extern MGVTBL PL_vtbl_backref;
PL_vtbl_backref->svt_free = MEMBER_TO_FPTR(handle_killbackrefs);
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