There are two reasons why x86 Windows would eat battery.
First, Intel's processors are not power savers. They eat power. They consume power to perform computations, they consume power to cool themselves down to keep from overheating when computing. Just having to translate x86 CISC to RISC on the chip before doing the computation is an additional step that uses power. Even if Atom can turn itself off when idle, it cannot avoid the x86 overhead.
Second, Windows is a resource hog. It was never a very well-coded OS. It was open, and popular (due to its DOS legacy as a result of IBM), but not written with efficiency in mind. And not only that, but with Windows running, the machine will never sit idle. It'll always be doing something in the background.
But Windows 8 isn't going to replace desktops with tablets at work anytime soon. Hell, work machines aren't going to replace Windows XP and 7 with Windows 8 at all, whether on the desktop or some other form factor. It's not that Microsoft declared war on their hardware partners. Instead, I think they declared war on the user. Their hardware partners are just collateral damage.