When I do that, it destroys the actual UIAtlas prefab (or the UIAtlas component itself if you target that with the destroy) from the project completely. If you meant Destroy the UISprites that use the atlas I want unloaded from memory, I already tried that and then called Resources.UnloadUnusedAssets but it did not result in a release of memory.
The only way I have successfully been able to release memory used by atlases is change the scene or unload the textures used by the atlases, but that makes them unusable until I restart the game.