First of all, I hope you love Atlanta. It's got a horrible infrastructure but everything else is nice.
To agree with a few posters above, Cafe Sunflower is fantastic as is the Flying Biscuit. It's a shame your visit wasn't two years ago; there was once a place called Lush that offered entirely vegan cuisine. Another option around Midtown would be Soul Vegetarian off North Highland. If you can get out of the Perimeter a few places to try would be Harmony Chinese (all veg), Three Bears Cafe (Marietta), and ThaiCoon (again, Marietta).
You'll find that many restaurants, especially in the city, have veg options available.
I second the fact that most midlevel to upscale places in Atlanta are veg-friendly and will have a few entree and app choices for one to pick from. I tend to order veggie-centric dishes. I can say that I loved the beet ravioli dish at The Globe (which is in midtown) recently. You could also do Woodfire Grill - they have a wonderful vegetable plate that I often choose over meat dishes when I go. Most places worth their salt in Atlanta will have something delicious for you to eat.
But don't you find Cafe Sunflower terribly noisy? I haven't been there for awhile (for that reason) but I SO wished they would figure out how to deal with the accoustics. I agree - the many wonderful little restauarnts by Atlanta's (and Decatur, Marietta, etc) talented young chefs will easily accomodate vegetarians. Just ask.
Let me also add Beleza to the recommendations below. It's fairly new...located on Juniper in Midtown...and is a very cool spot that has great cocktails and wine...and a very unique, healthy menu. Lots and lots of vegetarian dishes - I think the only animal on the menu is the fish, which is done sous vide. Smallish plates so you can order a couple and try a few things. I dined there and enjoyed it a lot.
When I was about 15 (about 14 years ago) my parents became vegetarian and I have been to a lot of restaurants around town that cater to this cuisine.
I would strongly suggest that you check out Cafe Sunflower (on Peachtree Street), R. Thomas is good, then there's also The Flying Biscuit Cafe (not 100% vegetarian but they do have some offerings.)
I put The Flying Biscuit on there because you mentioned midtown. I think their food is bland but my wife likes it.
Good luck and let me know what you thought of these places. I'm curious.
(some more upscale restaurants in the area also cater some dishes to vegetarians: The Food Studio, Ecco, Table 1280 at the High Museum).