You make a very good point: the use of nuclear charges for propulsion would never be allowed outside of highly-restricted and secure government operations. Even if one designed the charges so they had to be detonated by some large onboard system (as opposed to a small, self-contained bomb that could be stolen and used for terrorism), the charges would still contain fissionable materials that would have to be closely guarded.

I once had some hopes for inertial laser fusion systems, which use charges made of more benign substances (especially if one can get away from a tritium requirement), but I don't see this process working even on the ground yet.