MCO has the best system for returning rental cars from rental car companies in the airport. You jump out of your car, grab your stuff, and go across the street to check in. It really only takes 1/2 hour to get to MCO. Everything is so well marked. I would leave yourself enough time to get to the airport so you have 90 minutes until flight time.
I would definitely take the car back to the airport, not the magical express. Sometimes ME is picking up people 4 hours before their flight time. This is ridiculous. Trust me, taking the rental car back will be alot more efficient. I have done this many times since we always rent a car in Orlando. My last trip I left Universal Studios 2 hours before flight time and had plenty of time. The only thing bad about SW is that everyone uses the online check-in so we ended up with C passes, but still sat together.
I was going to do the same thing as you - ME to the resort and rental car return, but decided to go rental car the whole way.