Sure, why not? I haven't actually done it, but in the mods section it looks like changing the rotors at least isn't that much of a problem... you're already halfway there or more by taking off the big wheel anyways.
Of course, if you have bigger calipers or something that won't fit the smaller rotor, then you'd have to swap out the whole assembly and rebleed the brakes and stuff I guess.
I think the STi 4-pot big front brake kit is about the biggest you can get on the 16" rims. My friend has a set on the stock MY00 rims and they look real sweet and fill outt he wheel very nicely.