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.
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...
According to A. Einstein you shouldn't be able to tell the difference between two inertial frames of reference. Physics would behave exactly the same. So if you don't hit your exhaust in the first instance you won't in the other either.
You don’t fly into your exhaust until you accelerate enough to start going in the opposite direction. If you’re driving down the road and throw an apple out the window behind you, you don’t run over it if you put on the brakes, you’d have to accelerate to cross zero velocity and then start going backwards to catch up. An apple will just sit on the highway, rocket exhaust will be moving with quite a bit of speed as well.
Your analogy isn’t really valid, because in the rocket situation you’re flipping the rocket and throwing exhaust forward to slow down. That would be analogous to throwing apples forwards, not backwards.
