You couldn't just turn around....

... but you could shut off the engine halfway[1] and then disconnect the engine and reattach it at the front. You could also, in the early stages of the flight, excavate fuel from the cometary nucleus such that the instrument package is buried deep inside; and the fuel would be removed from the aft end to maintain as much shielding as is feasible for the high-speed part of the journey. The goal would be, upon arrival, to have a slender chunk of fuel left over (reinforced by fuel delivery tubes), with the engine at the fore end and the now-uncovered instruments aft. There is really nothing that could be done to absolutely protect the engines in the deceleration phase of flight; there would have to be enough small-ish engines that redundancy could handle the loss of a few from collisions whose damage can't be repaired.

[1] You would actually continue positive acceleration past the exact midway point, since the decreasing fuel mass would result in much greater acceleration magnitude at the end of the flight.