Late to the party on this one, but I like the idea of infrastructure purchases. Much better than what we have now, I would say.
It'd be difficult to balance, but here's two options:
A) Ridiculous costs, requiring a good segment of the entire Faction to pour resources into the area, which would take a long, long time, but would make the area very, very valuable... and paint a huge target on the area for every faction to see. It'd have to last for a while, but it'd last long enough to make the buy worthwhile.
B) Gold increasing time and buffs for an area, so that pouring increasing amounts of gold into an area would increase it's buffs as well as the duration of those buffs. This would allow a single player to have an impact on an area if they were to grind out a good deal, but it would also mean that a faction could work together to make one area practically impregnable and very valuable, or could work together to make it's borders highly efficient and well defended.
C) Seperate buffs that you can buy at reduced prices, but at lower tiers, and with only so many you can have active at a time. For example, let's say you have three possible buffs, Cost Reduction, Resource Yield, and Defenses. When you go to a section to choose the bonus you want to spend gold on, you see which buffs are currently active, and how close another buff is to being 'bought'. You could only have 3 buffs active at a time, so you could potentially have one of each, two of one and one of the others, or else specialize an area for a very powerful buff. That would make it possible for 'infighting' amongst the factions, as competing leaders would try and make an area more efficient, make it easier to defend, or reduces the price of certain things when defending a nearby sector.
I kind of like the third option. It'd be fun to watch, and well organized factions would be able to pool their resources to stabilize their borders, or else make areas within their borders extremely valuable while they own it. I would say with the duration... maybe only until you lose the area? Since this is a war, and infrastructure would be destroyed, it would make sense, but some of the value might be recovered. Say you take an area with all three buff slots taken, a small amount of value would go to the conqueror.