There are shaders that can create a normal map from a diffuse texture map, from memory there is one in AMD(ATI) RenderMonkey, but sure you can find plenty of other examples online.
So one method (I guess you need Unity Pro for this though), is to use the shader with renderToTexture to generate your normal mapped textures at runtime. This should be very fast compared to get/set pixel.
Alternatively you can use get/set pixel and simply convert the shader code into javascript/c#.
Edit: You might find this page useful for obtaining better quality normalmap data.
