I assume that JetBlue is making this offer for the same reason that any airline offers a discount tied to an abnormal schedule: they can’t sell enough full-price (or even normal-discount-price) tickets to fill their seats during September, but they don’t want to reduce the number of flights they offer, and once they’ve committed to flying the plane then the marginal cost per passenger is trivial.
In other words, the plane is going to pump out those greenhouse gases whether it’s half full or three-quarters full, so your decision to accept this offer isn’t going to make much of a difference.
Well, it'll pump out slightly more greenhouse gases when it has to support the marginal weight of one additional passenger. But the marginal energy expenditure for one passenger is most likely pretty thin.
Edit: Changed from "impact on the ozone layer".