Try this using a two stage missile as Cocyte did, I think that may be your problem. (I've done the following with active and thermal sensors, though not yet geo/grav, it's a bit too micromanagy for my taste)
First design a bouy to hold your geo/grav sensors, check the "No Engines" checkbox.
Second design a delevery system with an efficent engine and the above bouy as a second stage, set the seperation range to 0.
load up the missile in whatever ship you're using, place a waypoint on the planet. target the waypoint, tell the FC to open fire, advance time a couple of seconds, and remember to tell the FC to cease fire so you don't waste those expensive missiles by firing your whole wad at one waypoint.