Some possibilities. Further down the road, they needed that aircraft in Orlando, to then move on somewhere else. Possibly affecting many more passengers than those missing their JFK connections. Another reason could be crew rest, a crew close to timing out on hours.
The decision was made higher up at dispatch, by someone a lot higher on the ladder than the CSA's at the airport, who has to look at the overall picture. One plane out of place can start a cascade effect through an entire route, affecting hundreds of passengers.
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