Thank you for your answer.
I have followed your advice, turned the option on and created a template override for product/cart.php.
I've commented the code below (line 145 and 380) :
/* if($group && !empty($product->cart_product_option_parent_id))
continue; */
Now, the options are separated from the product and are removed from cart when the product is removed.
Unfortunately, it is impossible to remove the options independently. I neither can change their quantity.
Do you have any idea for fixing this ?