I dont own a 40d (yet) but can't you turn off the in camera noise reduction? According to the review you can only turn off the 'High ISO speed noise reduction' option but basic noise reduction is always on. This really sucks because it is almost like shooting JPEG instead of raw with a loss of detail that can't be recovered.
Using custom Function C.Fn II -1 and C.Fn II -2 you can disable / enable both Long Exposure Noise Reduction and High ISO Speed Noise Reduction.
Not sure what you mean about 'basic noise reduction'? If you mean the inbuilt functionality of the sensor to minimize noise, this is present in all DSLR's and is not an option.



