They can fly the CS100 from both ATL and JFK with the existing runway. They are however going to look at many factors before they would enter the market.
Things they would consider is how much traffic do they cannibilize from the STT and SJU markets? Cost of staff and contract maintenance in EIS. Schedule reliability without a instrument approach. Wet runway operations. Passengers airport fees. There are a lot more smaller issues. I don't think in the end they would do it however I am told marketing loves the airframe and already has 18 new city pairs they feel they can fly that currently don't have non stop service.
If they ever actually lengthen the runway the 757 operates just fine from SNA to ATL off a 5700' runway.