I suggest you go with a private tour company like Alla or Den Rus - they will include one camera permit for the sites where it is needed. We only needed them for Church on the Spilled Blood and St Isaacs. Everywhere else you could take as many pictures as you wanted including inside the palaces and the Hermitage. We went with Alla Tours and cannot prasie them highly enough.

Extract "One has to buy a ticket (prepare 130 rubles plus 50 for a photo permit), and then wait till a group of 15 is formed. Tickets are limited: we arrived at 11:30 and entered the last “wild” group on that day. After us, only pre-booked groups were allowed, arrived by tour buses." So looks as though this covers the area as there is strict security. 180 robles is around £4 so not a great deal. So you can go individually or go with a group from the ship, probably the best option ?