If I do salmon en croute I keep the salmon raw. I have done it with individual fillets and whole sides of salmon and always keep it raw. I marinate it first and lay it on spinach leaves,then the pastry. By the time the pastry cooks,the salmon will be cooked. If you par-cook it first it may be over-cooked.
Any meat en croute is different.You need to sear/seal the meat to keep the juices in or you will have a soggy botty!