Hey Don,
I've done a short SC Greek Isles 4-night sailing roundtrip from Athens in 2016. The three ports we visited were Santorini, Mykonos, and Hydra. We did not take any Clipper tours, preferring to do our own thing. It helped that we had been to most of the ports of call before. In Santorini, we rented a car and drove around. Mykonos is easily done by foot, plus an early ferry ride to Delos. In Hydra, we booked our own private tour with Harriet's Horses in Hydra and did some walking ourselves independently afterwards. I probably would not try to organize things while onboard. There aren't that many passengers on the ship (fewer than 200, in these COVID times, I think it's likely you'll have fewer than 100 on your ship). In the past, I would generally try to plan my own days taking public transportation - in Greece, it's relatively easy to do, at least pre-COVID, with the help of the Greece CC ports of call boards. Nowadays, if I was going on SC, I would probably still try to do my own thing, but I would be open to taking Clipper tours, for places where I have not been before and where I don't feel taking public transportation.
Hope you enjoy you SC sailing! The first time, waking up, being low on the water, entering the caldera below Fira/Santorini, is truly something special!
Cheers.