I don't really see a problem. True, you can't minimize the game window using a minimize box, but you can Alt-Tab to any running application (which minimizes the game window) or you can Ctrl-Esc to the start menu (which also minimizes the game window). Once the window is minimized, do whatever you want, then, when you're ready to go back to the game click on CTP II in the menu bar at the bottom of the screen.
I hate the fact that all the new civilization games have gone to full window mode. I love civ 2 and the fact that i can respond to my icq and check my email and surf the web when its not my turn. But even when i am playing single player i have the chance to do other stuff etc. Who else likes/dislikes the fact the game is played full screen?