There are a few differences. The most notable difference is the much larger distance that a Falcon 9 must go to achieve it's orbit. Also, the fact that Falcon 9 does a soft landing as compared to the fast landing required by a BM. Also, the Falcon 9 relies on GPS navigation, whereas a military system cannot be solely reliant. Lastly, these systems won't actually give their real accuracy, just vague terms like "pinpoint precision", but an open source claims the Tomahawk missile has an accuracy of about 30m. This is the most comparable weapon I know of to the Falcon 9.
As was noted, the accuracy of the Minuteman is estimated to be around 100m. Given an estimated 6 km/s, that means that it had to explode within 1/60th of a second, assuming pinpoint precision. Furthermore consider that a Minuteman doesn't have to be more accurate, 100m won't make much of a difference, so they don't have the required precision that a Falcon 9 landing requires.
The most directly comparable landing would be for the Dragon's landing back on the ground, but again, the speed at landing will be quite different. I suspect still that SpaceX will be more accurate, but as declared above, that doesn't matter.
Another compatible value is the orbital insertion error, which is estimated at 500m for the ORBCOMM mission in 2014.