We did exactly this with Budget a few weeks ago. We arrived on a Thursday night, picked up our car from Budget at MCO and drove it to WDW. We kept it there until Saturday morning, when we drove to Port Canaveral. DH dropped us off at the port and then went to return the car to the Budget office (about 5-10 minutes from the port). They had a shuttle to bring him back. Do allow an hour or so for that process, he said the line was awful and it is a small office (1 person working the counter).
When we disembarked the following Saturday, it was very smooth and easy. We got off the ship with our luggage, went across the road to the tent thing they have set up and ended up getting to put our luggage straight into the Budget van that was there waiting. It took us to the office and we got another car there that we returned to MCO the same day. Pretty easy, all around.
I would also definitely check Mousesavers for discounts - your estimates sound high to me. Just for comparison's sake, I used Mousesaver's discounts and reserved about 4-6 weeks ahead - we had an SUV for 2 days for $98 something with unlimited mileage. On the way back we had an SUV for 1 day with 150 miles free for $56 something.
Our shuttle driver on the way back did say that rental cars were pretty scarce in Florida right now, as many of them had left the state during the hurricanes and that residents that had damage to their own cars were driving them. I was very glad I had booked before all of those hit. Maybe that (and the time of year) has something to do with the prices you're seeing?
Carla