Re: BP plugins are visible and activatable for non-admin users in their consoles
There should not be any issues. However, I would instruct all Site Admins using your plugin to manually deactivate, upload the new version, and then manually reactivate.
Even if there were a few members with blogs that for some reason activated the plugin on their blog (per blog plugin activation), WPMU runs a check to see if any plugins that used to be per blog activated are now site-wide plugins. This means that WPMU will deactivate the plugin in the corresponding wp_x_options table of each user blogs.
For more in-depth information, see the function check_is_wpmu_plugin_on_activate in mu.php.