I am really sorry you have had problems. At the moment the DDL changes are not wrapped an a transaction but my understanding and experiments indicate that DDL operations are not transactional. In fact, if you run a DDL statement it seems to commit the current transaction. This is using InnoDB on version 5.1.45 (I haven't tried it on other storage engines/versions). If I am wrong please let me know!
If you know what caused the synchronization to fail please let me know and I will try and fix the bug!
Red Gate Software