I have finally captured another civs capital and I have to concur that it has done very little to affect them (aside from removing a major city = source of income, science, and trade).
However, this is probably due to my military strategy. How is that you ask? Simple.
When I attack a capital, I make sure that my flanks are secure. So, before I actually attempt a capital, I will take out surrounding cities first, garrison my forces, and then once my flanks are secure, I take the capital (at least thats how I did it this time, and thats how I am going to take the next one).
When I finished there were no "scattered" cities to be affected. I had counquered all the cities to the west and north of the capital. When they relocated the capital to the east, it was admidst all their remaining cities, thus it was no very important.
However, I think "giving" a civilization a "Free" capital once their main capital is taken is a crock of crap. A capital not just leadership. It is an established structure full of bearocratic buildings, legal libraries, etc.. It should have to be "rebuilt" and the rest of the nation should be stricken with corruption and unrest until they rebuild a capital. This would put a nice "spin" on warfare, and at least make the AI or other players be more willing to negotiate for their capital back.
ironfang