I grew up in Savannah and did a lot of diving there, and always enjoyed it. Most of the diving we did was at Gray's Reef National Marine Sanctuary, the Snapper Banks, or one of the many artificial reefs off shore. All south of Hilton Head.
I'm not sure what they mean by "shallow" diving..... There is no good viz until you get a way's out, therefore most of the diving is relatively deep, 60 or more at the closer in artificial reefs and 80 - 100+ at the Snapper Banks.
There is actually some very good diving off of Savannah, looks like you just got hooked up with the wrong crew. The Diving Locker in Savannah has been around for over 30 years and would probably be a good point of contact for anyone looking for information about diving the Savannah area.