You can do the same on a desktop app too, but it is less commonly done. To further avoid confusion, try make sure the pop-up modal appears over the parent window that it is blocking input for (this may mean coding your own window instead of the platform default alert/confirmation box, if the call to open one doesn't allow positioning information to be specified). I've seen alerts/confirmations pop-up on a different screen to the one that the parent window is on which makes missing it much easier (especially if the other screen is away from the main one, perhaps it is being projected at a wall for a demo). To further help: if the user clicks the disabled parent, move the pop-up to where they clicked – usually the title-bar or other chrome on the pop-up flashes in this case, but that isn't helpful if it is on screen 2 and the user is staring intently at screen 1.
