I have cruised the Med several times late in the season. The answer is, no it is not too cold to enjoy yourself. Actually, it all depends on what you want to do on the cruise. If you want to enjoy hot sunshine on the beaches and by the pool, then summer would be a better choice, but if you want to sightsee, late in the season is the best.
It gets hot in the summer in the Med and that makes it a bit uncomfortable to do a lot of walking, riding and sightseeing. The fall brings cooler temperatures that make the task much more enjoyable (not to mention less crowded).
Have a great cruise and let us know how it goes.