If you flip around and fire the engines to decelerate, you would be flying into the exhaust.
Edit: Actually this hurts my brain. If you're going 1,000,000MPH and fire propellant at 500MPH in your direction of travel, it would travel at approximately 1,000,500MPH and you would decelerate below 1,000,000MPH, so you actually wouldn't run into it. There's no drag on your exhaust in space like there is in an atmosphere...