[quote=@Isotope]
If you want to poison thousands of square miles with every flight O.o
[/quote]You say it as if that's a big number compared to the size of countries. Not to mention other factors.
Actually the shockwave of a mach 3 skyscraper flying close to ground would be far more grave than any concern about spreading some radioactive materials in the vicinity.
Acquiring lethal dose of radiation is both extremely hard and too easy. Layman guesses tend to be between these two extremes of mistake. In case of radioactive fallout of nuclear devices it's almost assuredly the former.

That and there's absolutely no need for the engine to be in contact with the reactor like Project Pluto did. Well, earliest methods may do that in order to make the design lighter/simpler but later developments can pretty much eliminate this. The only one threatened by radiation would be the pilot which is why a cruise missile is a good idea with it.