The AI is always "thinking" about its turns, even while you move your ships about and study your planets. This is a new feature in general gaming. It also uses all the cores it can find to do its thinking. This is the usage levels you are seeing. When you finish your move, the game uses the decisions already made to start moving AI units, thereby eliminating the delay for the AI to think before making its move. The reality is that you are used to games that were so inefficient they left your CPU idle >90% of the time. GalCiv3 has fixed that and you will probably see that move into other advanced game titles now that Stardock has set the precedent. Part of it may be 64 bit code, but mostly it is about properly using multi-core platforms.
It is, however, an awakening to see the change in your performance reports, so your surprise is easily understood. Imagine all your games being this efficient. It should get interesting.
As a point, your CPU is always busy. It is just that most of the time it is wondering what to do, "Has she pushed a button yet? Has she? Huh, Huh? Maybe I should try some defragmenting if she's not busy. I wonder if there is anything new on the network port. Gee, I hope we get to do some more cat videos today." and on and on. It makes no difference if it is playing a game, doing a spreadsheet, solving quantum mechanics equations, or just twiddling its digital thumbs. Think of the CPU usage stat as a sort of boredom monitor for your computer. 
