Jose on "Loading jQuery & javascript in footer"

You could try:

function load(){
    wp_enqueue_script( 'jquery', '', '', '', true );
    wp_enqueue_script( 'bootstrap-js', get_template_directory_uri() . '/js/bootstrap.min.js', array( 'jquery' ), null, true );
}

As you said it may cause some issues with plugins. That's one way I can think of but I haven't tried it yet. :)