Disconnecting and capping the IWE vacuum lines will keep the hubs locked and engaged constantly. It does not mean that the vehicle is always in 4wd/AWD all the time. The transfer case can still be in 2wd mode and thus not send pwr to the front axle. Keeping the hubs engaged all the time would, as you mentioned, possibly reduce fuel economy.
I am surprised this is Ford's "fix" for this. They must know that the system is inherently faulty or they would just replace the IWE itself.