It would be nice if HADOOP_CONF_DIR could be set in the environment like YARN_CONF_DIR. This could be done in lib-exec\hadoop_config.cmd by setting HADOOP_CONF_DIR conditionally. if not defined HADOOP_CONF_DIR ( set HADOOP_CONF_DIR=%HADOOP_HOME%\etc\hadoop )
A similar change might be done in hadoop-config.sh Thus the bin could be under Program Files, and Program File be locked down from modification, but the configuration files still would be in a separate director. (--config didn't seem to work for namenode)