Here is the solution:
In the GetOutput implementation I used the IMILBitmapEffectRenderContext.

To take the area of interest into account, I got the
IMILBitampEffectRenderContextImpl from IMILBitmapEffectRenderContext.

Code Snippet    
//**********************************************************************
   // Get our render context's implementation interface
   //**********************************************************************
   CComPtr<IMILBitmapEffectRenderContextImpl> spRenderContextImpl;
   if (SUCCEEDED(hr))
   {
       hr = pRenderContext->QueryInterface(__uuidof
IMILBitmapEffectRenderContextImpl),
            reinterpret_cast<void**>(&spRenderContextImpl));
   }





Then, I used the GetOutputBounds method of the
IMILBitmapEffectRenderContextImpl.
Using that, I can apply the effect only to the output bounds specified by
the BitmapEffectInput.