I tried to do exactly this with my pre-order a few weeks ago.
Basically, they can't just change the color for you. I had to have the order cancelled over the phone, but in my case, this didn't automatically reset my subsidy eligibility with AT&T. I had to spend a couple of days on the phone with AT&T and Apple, waiting for it to be resolved. Apple eventually was able to reset it, and I ordered a black one.
I ended up returning the 3GS 2 weeks later in favor of my 2G iPhone (saving my subsidy for a bigger update next year), but I digress.