I think that the reasoning behind this rule is that when the ball is deflected, it can suddenly and unexpectedly change direction. When that happens, a fielder toward whom it is deflected may suddenly and unexpectedly change directions to go after it.
So, we cut the runner some slack and acknowledge that when a fielder suddenly and unexpectedly moves into your path you might not be able to avoid her.
But why do they exempt a deflection by the pitcher from this rule? Who knows...it doesn't make sense.