A couple of simple ways to make it more friendly
1) While the AI is thinking the computer doesn't monitor Alt-Tab. I'm playing several AI's on a big map, the turn calculation is long enough that I'm switching away and doing other things while it thinks. If I'm quick I can hit end turn and then Alt-Tab and in a few seconds the game will hide itself, otherwise it won't until the AI calculations are done. Even if I'm fast enough, it still won't release the mouse until after the AI calculations are complete, though. (Note: This mouse problem can only be observed on multi-screen systems.)
2) When the game is simply down on the taskbar, how about changing the title to show if it's calculating or waiting for the player.
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