Sanford most likely will cost more in the long run. We have flown there twice. The airport that flies there is about 10 minutes from my house, while iof we fly into MCO direct we have to go about an hour to the airport. My DH prefers just going out of the local one and WANTS to rent a car, even though we rarely use it. I really liked it the year we flew into MCO, using ME, etc. But DH felt like he was being control or something. The price going into MCO for us was actually cheaper, but we got a great deal that year. The years we flew to Sanford the flights were really close in price and then to rent the car put it over.
Allegiant isn't a bargan like you think either. It is 30 round trip per bag. It is like 13-15 dollars per person per flight to pick a seat (which we do to ensure we are all together with DD.) and another $5 for priority boarding, which we don't do, but they act like you should.