How to apply wordpress ‘with_front’ = false for categories?

The register_taxonomy_args filter should do the job intercepting the arguments for the specified taxonomy:

add_filter( 'register_taxonomy_args', 'cyb_modify_category_args', 99, 2 );
function cyb_modify_category_args( $args, $taxonomy ) {
    if( 'category' === $taxonomy && is_array( $args ) ) {
            $args['rewrite']['with_front'] = false;
    }
    return $args;
}