As we know allies retreated as far as back to the Marne, leaving north of France unoccupied. Why didn't the Germans take advantage of this?
Well a few reasons:
It wouldn't have made that much of a difference. There were some odd 150,000 British troops on the mainland who arrived well before the Germans made strides into French territory and that was, basically, all the British had at the moment. The Territorials would not make their way to the mainland until December 1914 at the absolute earliest and 1915 for more than half. Considering the Marne had over 2,000,000 Frenchmen in it, the British were by no means the key ingredient to neutralize. It was the massive French army.
There's absolutely no reason that blocking the ports means that either the French can't support the relatively tiny British Expeditionary Force or that Britain can't simply just use another port. They had the largest navy in the world. They would have just landed supplies and men in La Rochelle or Marseille.
It was counter to very fundamental purpose of the German plan. The point of the German plan was to rapidly seize Paris and encircle the French military in approximately a month to force an early armistice in the West so the Germans could have their war of reckoning with the Russians. The Russians were their major threat and that's where they felt the war would have the most fighting, and in many ways they were completely correct.
Ultimately, and I feel this needs to be repeated often, real life is not a video game. You aren't sending in a 'stack' of troops that you can 'split off' to go occupy some undefended provinces or something. Even ignoring the fact that by the time the Germans were nearing Paris they were at 50% strength, sending troops requires massive logistic trains, stay behind forces to secure supply lines and the front all the way there, and risk being cut off and destroyed by enemy forces. Ultimately that wasn't a luxury the Germans had considering their situation and further it was one which just did not make sense. They would have to travel nearly 250-300km to...do what precisely? While they barely manage to hold on from the French counter attacks?
Ultimately I feel what's best is for you to read a book which properly contextualizes both sides plans and both sides positions at this critical point in the war. For that I'd recommend Holger Herwig's The Marne.