I'm not sure of any way of doing this "cleanly". It's the same as any other OS in that the ESX(i) is running when the server is on (after POST). You're not able to put it in a mode that is "safe to shutdown" like the Windows 95 days! 
You COULD do it not cleanly by putting the hosts into maintenance mode, but then when the UPS(s) drain empty the server will go off cold, probably not a good idea, but maintenance mode would be better than letting all your VMs hard shutdown too.
About the only thing I can think of is to shut the server down as normal, and then boot it up into the BIOS (or hit the pause button when it's POSTing) and leave it there.
Any others have a better way of achieving this?
Cheers,