Well, presumably you wouldn't be accelerating just before you want to slow down, so the atomic bombs wouldn't be recently detonated and their debris wouldn't be nearby.
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...