It's likely (maybe even confirmed as far as I can tell) that all patching will be done through steam. Firaxis/2K have even said it's one of the big advantages of moving to steamworks - they only need to patch one version of the game.
How the game will patch should probably not be a factor in deciding where to buy the game from. The main thing is if you want to download the game or not (and hence decide between a disc vs. download purchase of the game).
How the game will patch should probably not be a factor in deciding where to buy the game from. The main thing is if you want to download the game or not (and hence decide between a disc vs. download purchase of the game).