“Allow this device to wake the computer” option disabled

You could use /etc/rc.local or some system boot scripts, but this wouldn't be the best way to do it. On startup your network interfaces are configured, sure, but there are other times when your network interfaces may be brought up or down and you will need this executed during those times.

You want to edit /etc/network/interfaces:

You should have a line like:

iface eth0 inet static

Underneath that, indented further, you want to create a post-up and post-down commands e.g.

iface eth0 inet static
    post-up /usr/sbin/ethtool -s eth0 wol g
    post-down /usr/sbin/ethtool -s eth0 wol g

Obviously, replace eth0 with the relevant interface if different.

See interfaces(5) for more information on post-up and post-down commands

man 5 interfaces

So from everything I have gathered, there is not a way to do this. From what I can tell, the magic packet doesn't differentiate between sleep and powered down.

That doesn't mean remote support is impossible. You just have to attack the problem in another direction. The core tool that you have to overcome this limitation is scheduled tasks. When you create a task, there is an option under "conditions" called "Wake the computer to run this task". This will allow you to run a task when the system is in sleep mode. If the computer is off, it will skip over the command and stay off.

Once you have your tasks setup, just setup an automatic statup time that happens before all of your tasks and you will be able to again manage your systems.

I use "schtasks.exe" to add tasks remotely. It allows you to specify a username and password to use for the tasks and you can overwrite them as needed.

It's a complex system to setup, but can save alot of time and power if you have windows 7 machines across the board.