first, I set the variables at the top of the plugins .php file i wanted to be global. The file is very well noted by the author, OMG thank you! Very easy to control what variables the plugin activates with thanks to great coding and thoughtful notation.

Then I changed the function that mails lockout notification to the administrator, so that it will email the super site admin(me) rather than that particular sub blogs admin.. what i did was modify the get_option in line394 to say:
@wp_mail(get_site_option('admin_email'), $subject, $message);

Then, i changed the code where it constructs the plugins dashboard submenu. I changed it so that it would show under the site admin menu instead of settings. that way only the super site admin can see it and not the sub blog administrators. I changed Line 607 to:
add_submenu_page('wpmu-admin.php', 'Limit Login Attempts', 'Limit Login Attempts', 10, 'limit-login-attempts', 'limit_login_option_page');

Then I used the plugin manager to auto-activate the plugin for all users sitewide.. that way any newly generated blogs will automatically activate the plugin with the settings I want, and having moved the menu, users cant modify them.

It is important to note, that if the plugins menu is accessable to your users, they can deactivate the plugin. Rather than attempt to solve this, i will just hope that my users are not that stupid.

hope this helps...

oh, the settings I changed to my likeing were;
login attempts moved to 5,
lockout time decreased to 15 min.
lockout log settings changed to 'log, email'
and notify email after 1 lockout