BuddyPress.org

An index.html is fine, just go to http://yoursite.com/index.php to reach front page. Bad thing is that if someone knows your site is WP/BP, they would just go to http://yoursite.com/members , /groups/ or /about/ and they could see the pages if you’ve enabled the components.
Maintenance Mode plugin works with WP/MU/BP. Thing is, it interferes with media uploads via BP plugins like BP Gallery or BP Album but it doesn’t interfere with media uploads via Post/Page panel. Good thing with this is that even if outsiders try to access site via http://yoursite.com/members etc, they won’t be able see the page/s and get redirected back to Maintenance Mode front page.