Is there a way to limit the requesting users email to a particular domain, ie just .mil, or just .edu?
Topic on Extension talk:ConfirmAccount
You can possibly edit MediaWiki:common.js to run of Special:RequestAccount pages (using the mwconfig->get( 'PageName' ) JS variable). It could check the field onChange and show an error and disable the submit button. Requests that make it through anyway (e.g. JS disable) could simply be rejected.