Interesting review. You are probably aware that we are somewhat "tour adverse" and spend a lot of time helping folks do their own thing. We big HA fans but seldom use their tours. In fact, on a recent 41 day Prinsendam cruise we managed to escape without a single excursion. Regarding the prior review here are a few thoughts for future cruisers.
Venice- It is very easy to hire your own Gondola at any of many gondola docks. The going rate is about 90 Euros total and for that price it can be just the two of your (or 4). We will usually buy a bottle of wine before getting on a Gondola and have the cork pulled. Then, we glide through the canals sipping some nice wine. For those that spend one or more nights in Venice it really pays to buy a vaporetto pass (they sell them for 24, 36, 48 and 72 hours) which give you unlimited use of the vaporettos. You can then ride out to Lido, Murano, Burano (our favorite), etc and around Venice for no additional charge. With the new people mover providing cheap transportation between the ships and the Piazale Roma (where there is a main vaporeto dock) it is easy to get around.
Pireaus - We assume the cruiser had been previously to Athens and was looking for something different. When in this situation we like some of the boat options right from Pireaus where you can easily grab a boat to Aeginia or perhaps Hydra. The high speed boats are within walking distance to the cruise ships and the islands are a change from Athens.
Istanbul - We agree that a good guide can be real helpful here and would always recommend hiring your own guide or just going it alone over an overpriced, overcrowded ship excursion. This city is actually pretty easy to do on your own if you like to walk (best way to see any city). There is a handy tram line that can take you from the just outside the port into town for about $1.
Santorini - We have never seen the need for any tour or guide on this island. Its easy to see both Fira and Oia on your own (cheap bus runs between the towns) and a rental car is a great way to explore the island for those that want to get out of the towns. They actually have some nice beaches on this island too.
Mykonos - Totally agree with the previous post. We usually tell folks to take the local bus to Paradise Beach and also spend some time exploring Mykonos Town.
Katakolon - This port drives us a bit nuts. Having seen Olympia there is no reason to return and this part of Greece is not full of good tourist destinations. If we ever return for a full-day we would probably opt to rent our own car since there is a rental car place close to the pier and they are pretty cheap.
Kusadasi - We always recommend hiring a private tour here which should include the "Terrace Houses" as part of the Ephesus visit.