Break out of wordpress filter

Yes, there is such way. All you need to do is to unregister your filter inside it:

function highlight_base_category( $classes, $item, $args ) {
    // most probably you have some if statement here
    if ( /* YOU CONDITION */ ) { 
        // your code
        remove_filter( 'nav_menu_css_class', 'highlight_base_category', 1 );
    }
    return $classes;
}
add_filter( 'nav_menu_css_class', 'highlight_base_category', 1, 3 );