Maybe I'm misunderstanding your question. But AMD doesn't have native support for Stereoscopic 3D in their drivers. It can be implemented with 3rd party software such as Tridef 3D. Are you saying you have Tridef 3D installed but it is always on?
The idea of disabling 3D Vision to reduce input latency is based on the fact that 3D Vision requires vsync. Vsync by nature buffers frames, and thus creates input latency.
Long story short, what you can try is manually disabling vsync. Obviously, this may bring about screen tearing, so you may have to choose between image quality and smoothness over reduced input latency.