Not much. The main difference between a missile and a robot controlled spacecraft is that the latter has more propellant. The spacecraft presumably is intended to return while the missile is just has to arrive at the target. The spacecraft will have roughly 4x the propellant [1] propellant to enter mothership to target trajectory [2] propellant to slow to combat speed at target [3] propellant to enter home to mothership trajectory [4] propellant to slow to a stop at mothership. A missile only needs [1].

A missile is likely to be more efficient and cheaper, by a massive margin. Otherwise, none.