For now, the point is moot because the game hard crashed and I had to delete the save. But RP-wise, I handled it that the military refused access to their base, because they didn't trust the wacky civilians who had designed and built the Geo Probe missiles outside the normal government processes.
Also, I have been trying to build a doctrine for using them.
In the home system, the overhead cost of magazines isn't an issue, but using them in other systems, it really is an issue. A bare bones drone, (size 2 geo drone head, size 1.5 MSP engine, reduced fuel use, .5 msp fuel), in a ship with 10 magazines, (the same cost as a geo survey sensor), means that a survey ship could survey about 40 planets/moons/comets before returning for reload.
But it would also have to be a military ship, so that adds costs for maintenance.
I think they are useful in a conventional start. Then you use them to survey the comets and Mercury, which can be annoying for a slow commercial surveyor. And use them to survey the widely separated rocks in the Ourt cloud.
But if you are building a commercial shipyard early, to get started on colonization, then you are prioritizing logistics techs over drive techs, so the essential ingredient for geo buoys, the reactor, comes later.