yes they will...a focus guy has a set of E1 wheels that he uses on his Focus SVT for winter. They fit under the wheels.
EDIT: I was lead to believe the Focus brakes are better than the stock contour...rotors might be the same size, but are the calipers not different? I need new rotors regardless...I'd like to get some extra stopping power as well, but nothing over the top (like an $800+ baer kit or something). If it's really not worth the trouble, can I get bigger rotors, or does anyone recommend the slotted/drilled BAT rotors? And perhaps some better pads (recommendations please)?