JFK-MSY is mainline so I'm less worried than if it was an RJ. I'd expect likely delays, but if you can tolerate getting to MSY a little later, I'd probably stick with what you have instead of adding ATL connection. However, since you have flexibility and there's waiver, worth looking at options at least. I would not change unless I could get confirmed seats on both JFK-ATL and ATL-MSY however. And if you do it, take an earlier JFK-ATL before the winds pick up midday.