Occupied military buildings make borders stronger. As you mentioned, old Settlers II had simple rule: you have to have occupied military building to have a territory on your side. Here, in Widelands, we stick rather to Settlers III way of territory: once you gain, you can't loose. Except conquering by other military building. The only difference is that sometimes you have complete fog of war which prohibit you from building anything new. So answering kapputnik: sometimes you have to leave towers (medium building with high range of view) inside your country. Without this you will lose your potential.
As I understand, your suggestion is to provide a possibility of changing state of working military building into not working one? That will completely change the way of playing. Imagine that you are playing on a rather small but hard-terrain map (example: desert tournament). On the front line there is a race between two fraction: who will have more level10 soldiers (see discussions from previous tournaments). But nobody can attack the other side. There is no place to build a tower. So the only way of seeing the enemy is to place a scout and wait until he will reveal some territory with military building. But the players can build small buildings like sentries or small towers. And they do that. If the military building contains level10 soldiers, they are rather safe. If not - the building will be conquered. I can remember few games like that. So for example king_of_nowhere built up several sentries and wait until he will have at least one free level10 soldier. After that he made everything he could to place this soldier silently (without enemy's notice). Tactics that he got was: 1. build a building and cut roads, 2. wait some time, 3. build road and get the proper soldiers. From enemy's side it was like: 1. build a building without road, 2. place a road, 3. soldier inside = attack. The defence is about noticing if any new road is placed around the borders. With your change, the defence is much harder.
As I understand, you found a good point what can be done inside your country. But this feature can make games even faster and harder to new players. Real experts in widelands don't need this feature . As kapputnik told, your economy doesn't hurt of several useless soldiers.
Sorry for a long text, hope you can go through it.