We have very good things about a tour group Red October in St Petersburg that will do van tours with an English speaking guide. They are able to take us without Visa's as they will have our passport information and will give it to the immigration office. We will be sent tickets in the mail and will have those for leaving the ship for the tour. We like the Red October tour itinerary and they are more flexible than the cruise line tour. Have you heard of this tour group?
I did this in 2000. Celebrity was very specific in that we would not be permitted to leave the ship unless we had Russian Visas. We had gotton our Russian visas ahead of time and no problem. I think using a private tour company is the way to go. We paid $70 per person for the visas from the Russian Embassy in US. Even with this fee we got a much better deal than the ships tour. We had a group of four with a driver and an English speaking guide. We were able to see quite a bit more since we move faster. We used the volkswagen type van as a taxi to one of the shows at night.
Again everytime we left the ship we had to go through passport control and they checked the visas.
We used Note Bene travel agency run by Nikita Zonan and I would recommend him. He speaks English very well. His e-mai address is <firstname.lastname@example.org>.
You could e-mail him and get a second opinion about the visas.
The ship's tour uses an all inclusive visa permit for the members of the tour. Possibly Red October is also doing that.