You disable automatic updates in an enterprise environment? You either have users that are much more attentive and technically minded then I ever have, or you have an office full of security vulnerabilities. I would guess a third possibility is that you have never been responsible for an enterprise deployment, and you're talking about a few home machines. Yes, that seems more likely.
It's utterly and completely trivial to design a scheme that's much better on the energy usage then "leave your computers on all night", and yet better vulnerability management then patching manually. WOL can (but doesn't have to) be part of this, but it's not three magic letters. Having overseen multiple enterprise wide rollouts of this, the biggest issues are enabling AND properly configuring directed broadcasts on each subnet, and changing BIOS settings to support WOL.
The first is primarily an issue because the type of people who build and maintain large networks aren't the type to make global changes on a whim, especially one that allows broadcast traffic to cross subnets. Also, depending on the size of the network and the centralized management options in place, this could mean hours or even days of work for them. Once you can get them to settle down and listen to the proposal (for some reason, they hear "broadcast" and tune out the directed part, as well as the "from specific machines" part), they generally get on board and use this as a point for deploying a centralized management solution, if they don't have one.
The BIOS Settings change is actually the harder one. Often, these setting are turned off in large environments, and depending on the age, make, and model of the hardware, may require upgrades, jumper changes, or other items. I oversaw one deployment where approximately 1000 machines needed a single wire connected. The time needed for this varies drastically based on specific machines in question and how much travel time the tech has, but for 10,000 machines in multiple small offices, 15 minutes per machine is not unreasonable. Travel time, introducing yourself, getting the user to log off, making the change, and moving to the next one. That works out to about 2500 man hours. This item right here is why many organizations choose to implement this feature on new machines.
Or, if you have the hardware to support it, it can be a simple SMS/Altaris/Unicenter SDO/etc job that changes the entire environment in a night.
Other solutions exist- Schedule wake ups, both with and without centralized management components. Intelligently designed power management profiles and patch management schedules. In an environment where no one leaves more than a few minutes early, and no one stays more than a few minutes late, you can get away with some very cheap to implement solutions.
I don't mean to imply that this is by any means hard- Any competent sysadmin type should be able to run the project. But it does require stuff like sitting down and thinking about it, actually knowing what the requirements are, and scheduling resources to be available.
Ditching windows and getting a proper OS would be great. I hate dealing with CALs. The cost of the OS itself often pales in comparison with the CAL price, especially when you start looking to upgrade say, your email server. If only one existed that wouldn't require sending 10,000 users to a training course to use...
(Note that's more a slam on corporate users then whatever OSS solution you prefer. These are the same corporate users that require a training class for PowerPoint. Further, their helpdesk/sysadmins can't even handle the relatively simple deployment of Power Management, how are they going to roll out Ubuntu, much less support it? Not that you'd care, as you're advocating a OS Change for enabling WOL, which is primarily a BIOS and Infrastructure level change...)