John, I think that idea of two separate playback configurations is good.
I use the Kampen I, Velosovo (demo) and the StAnna's organs, so I do have to change between sample rates.
I did tune the organs to A=440, though.
I did not know the sample rate would change the pitch, but I think this is because a program does not know which sample rate the hardware is working with? (I find that a bit foolish - just ask the rate from the Asio driver and conform the sample rate of the program to that.... But, as usual, reality is different.)
I am glad I finally know why this problem exists.