If you move the central axis of the ship model to just behind the nacelles, then the stretch effect will go in the forward direction only and not stretch the ship backwards. Failing that, create an invisible object bind the nacelles and pair the ship to the object, then stretch the object. It will stop the nacelles and the back of the ship stretching in the wrong direction.
If you move the central axis of the ship model to just behind the nacelles, then the stretch effect will go in the forward direction only and not stretch the ship backwards. Failing that, create an invisible object bind the nacelles and pair the ship to the object, then stretch the object. It will stop the nacelles and the back of the ship stretching in the wrong direction.
"Tom!!! Get us out of here."
"Vessel identified: U.S.S. Voyager. We will pursue and assimilate."