Waving aside the assertion that the only thing in space you might run into would be lonely protons...
My main issue is with your ability to "redirect" these protons. Since you are moving at relativistic speeds, you will have to induce the protons to move at relativistic speeds to go to where you want them to, quickly enough. And you will have an amount of time to do it in that is smaller than our ability to measure.
How does that work?