The list of active plugins is provided by wp_get_active_and_valid_plugins() during core load and comes from active_plugins option (multisite details aside).
While there is no explicit filter for it as any option it can be filtered via 'option_' . $option hook (so option_active_plugins) and mu-plugin (which are being loaded earlier) should be able to do it.
Note that it is more common and better practice to control what plugin does (such as thing it hooks) rather than if it loads completely.