Try adding pkgconfig as a dependency to enable libxml2 building.
--- trunk/dports/databases/spatialite/Portfile 2013-07-27 04:42:19 UTC (rev 108593)
+++ trunk/dports/databases/spatialite/Portfile 2013-07-27 07:26:09 UTC (rev 108594)
@@ -25,6 +25,7 @@
depends_lib port:sqlite3 \
port:geos \
port:proj \
+ port:pkgconfig \
port:libxml2
configure.args --enable-libxml2 --disable-freexl