I suppose you could have it come to a complete stop at a position, use the set-ship-position to make it exact, then use the set-ship-model SEXP to generate a bunch of pieces identical to the original while simultaneously switching the original model with one minus the movable pieces, and using the set-ship-position and set-ship-facing SEXPs to make them 'animate'. Then once all the animated pieces are in place, switch the ship model with the transformed one.
Depending on the complexity of the animation it might actually be doable too - like a gun extending or something.