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;
}