MD and the MPH applications are not usually reviewed by the same group of people, and they make separate decisions. Many schools don't require you to apply for MD/MPH concurrently (You apply when you're IN med school), so you don't have to do that if you're scared of the decreased chance of admission (plus it saves you time on writing extra essays).
I know for sure that Northwestern's MD/MPH application will not hurt or help your chance of MD admission. I got reassurance from the director of the MPH program there.
