Since no one has brought it up I'm going to mention the attrition system from EU3, which is pretty effective at resolving the SoD question in that game. SoD in that game are neither eliminated, nor fool proof. They exist but require care in their use.
The system works like this. Every province (if implemented in Civ this would be a tile) has a support limit. Say 9. Support limit is higher in provinces you own and lower in provinces your enemies own. As land tech and economic development go up this number increases, so by the late game it may be 30. You may place more than 9 regiments in that province if you wish, however if you do so you will suffer attrition. Attrition quite simply kills a fixed number of your troops every month.
So for example if a province has a supply limit of 9 and you march 30 regiments into it, some fraction of your army will die every month due to attrition. This represents the fact that the province cannot support an army of that size. The fraction of your troops that dies every month depends on the province itself, as well as the time of year. Generally it is 5% (so in a 1000 man regiment 50 die every month) but during winter or in tropical provinces it could go as high as 15%. Further, if you invade an enemies land they may scorch the Earth in that province, which could add another 10%.
What this means is that your SoD can be brought to it's knees by disease and starvation without the enemy firing a shot. Despite this a large army will always mop the floor with a smaller one, all things being equal. As a result you try to keep SoD's together only briefly, defeat the enemy army, then split your forces.
In Civ I think this could work quite well. In addition to grasslands having higher support limits than hills for example, you could have farms have higher support limits than unimproved tiles. Thus a viable strategy on defense would be to pillage your own farms in the face of attack by a superior force, to increase their attrition. Much like in EU3 you could imagine strategies of avoidance, where you keep sufficient forces near by to force your enemy to concentrate his forces, but avoid direct confrontation, resulting in attrition losses.