I downloaded and built the latest version (jboss-as-7.2.0.Alpha1-SNAPSHOT) from github.com/jbossas/jboss-as.git. The same problem is still there.
The edits to standalone-full.xml that are erased by this automatic rewrite are needed for MDBs to consume messages from a remote HornetQ server. My next attempt is to go back to EAP 5.1.