In Jetpack 2.6, we will introduce a new filter, jetpack_get_default_modules. It will allow you to stop the auto-activation of a specific Jetpack module.

Here is an example with the Widget Visibility module:

// To disable the auto-activation of Jetpack's Widget Visibility module:
add_filter( 'jetpack_get_default_modules', 'disable_jetpack_widget_visibility_autoactivate' );
function disable_jetpack_widget_visibility_autoactivate( $modules ) {
	return array_diff( $modules, array( 'widget-visibility' ) );
}

// Or, to disable the functionality in your own plugin if the user activates it in Jetpack:
if ( ! class_exists( 'Jetpack' ) || ! Jetpack::is_module_active( 'widget-visibility' ) ) {
	// It's not there, do as you like!
}

Reference.

If you wanted all Jetpack modules to be deactivated by default, you could use the following code:

add_filter( 'jetpack_get_default_modules', '__return_empty_array' );