Cruise ships don't sail into storms but navigate around and avoid them. We have never had to worry about storms as we usually don't sail in the fall. We have on several cruises when the weather had been some wet but the ships still port or tender unless the seas are to rough, in which case an island may be skipped. I have heard that if the storm continues, it could possible impact Florida on Late Sunday or Monday. Tropical storms and/or hurricanes are always a possibility at this time of year and the cruise lines are ready to respond to this.
Hope that you get out on time and the islands should be out of the mix by the time you are ready to visit them. Relax and enjoy the cruise, you will be hooked...