Let me explain a little about nuclear power. Fallout comes from radioactive byproducts of a nuclear explosion. A fusion reaction can only be caused by intense pressure and/or intense heat. The only way we have been able to provide enough heat to set off a sustainable reaction is through...a fission reaction.
Fusion is clean. When two hydrogen atoms (or dueterium, or tritium, which are variants of hydrogen that include neutrons) combine, they form a couple of different products, depending on the nature of the which forms of hydrogen are used, either helium or lithium, as well as neutrons and energy. Helium and lithium are not radioactive, and therefore do not leave fallout messes. Fission, on the other hand, is not so clean, the products of split uranium or plutonium reactions are quite radioactive, take years and years to decay to a safe point, and can get into the air or elsewhere to spread long distances with far-reaching effects. The reason nuclear weapons or reactors cause such lasting damage is because of the fission reactions that are used to trigger the reaction. If we were dealing with a reactor that did not have to utilize any fission reaction to trigger or sustain it, such as that used in the movie, it would not cause any fallout or lasting radioactive pollution.
Now, depending on the size of the explosion, we still have the issue of initial damage. The explosion would still send out highly energetic neutrons, gamma radiation, heat, and sheer explosive force. If it were a small enough reaction (as you might imagine would take place in a controlled reactor), then an out of control reaction would likely be relatively small. If the explosion took place far enough away, the damage it would cause might not be so lethal. That said, I don't believe that Batman could have possibly gotten far enough away in such a short time to get sufficient distance, nor do I believe 9 miles (is that right,?...Been a bit since I've seen it) would be a safe enough distance, as I believe even a small fusion explosion would be larger than that. So people in Gotham, at least those closest to the reaction, would be affected.
But bear in mind that exploding reactors in the real world, such as Chernobyl's reactor, did not produce a massively violent explosion equivalent to a bomb of a similar nature. It's explosion was rather small. But the radioactive damage it spread was really the deadly problem. So we can imagine something similar would take place in the movie.
I agree, it would have been best to avoid something like this, IMO. But I do believe that while it's not realistic, it's not the most grievous of unscientific movie mistakes. I'm okay with overlooking inaccuracy in movies if they are not outrageous, and this is not an outrageous error. It still fits in the suspension of disbelief I have established for the Nolanverse Batman series.