I took this information directly out of my 2009 unofficial guide to Disney World...it says
"When it's time to go home, you can check your baggage and receive your boarding pass at the front desk of your Disney resort. This service is available to all Disney-resort guests, even those who don't use Magical Express service. ( folks who have rental cars, for example ). Resort check-in counters are open from 5 a.m. until 1 p.m., and you must check in no later than three hours before your flight. At press time, the following airlines pariticpated in the program. AirTran, Alaska, American, Continental, Delta, JetBlue, Northwest, TED, United and US Airways.
Southwest Airlines doesn't participate, but the resort front desk or concierge will check you in online and print a boarding pass for you. You'll have to check any bags at the Southwest counter at the airport."
I can't locate anything about just taking Magical Express only on the way home. I would assume you can. I would try calling WDW to ask that question. Let us know.