Book wasn't a Shepard.
Jubal Early knew who he was, and knew to take him out, well, early.
He was deep UC for some reason or another, probably River related. Remember what River "saw" when she was in that fugue state with Book nastily saying "I don't give half a hump if you are innocent. So where does that leave you?" So it points to Book being on River's trail. When Whedon wrote the movie and tied up River's mystery Book became redundant and thus could be killed off for dramatic effect. Also in the movie, Book and the Op* never meet. This meant that all manner of plot and backstory awkwardness could be avoided.
Book's little hideaway had an AA gun, everybody treats this as routine. Yet nowhere in the series did we see any non-gov entities with heavy weapons. Serenity is unarmed, that magna-grapple pirate station didn't have guns, Rance Burgess had exactly one machine gun, Early's ship was unarmed, Niska's men did not have crew-served weapons or even grenades and his station was not obviously armed, and when Patience set out to bushwhack Mal and Zoe her and her crew have shoulder arms and hand guns, nothing bigger. And her knowing Mal I would think she would bring the big stuff just to be extra sure. Finally that moon that the Reavers attacked in Serenity obviously had no air defense of any kind.
So how and why did Book have a cannon and what strings was he pulling to keep it? Do you think the Alliance would be OK with a non-core planet having such firepower? They would have been all about taking it away, yet they didn't. A mere Shepard would not have been able to avoid that.
Now you could say that the Alliance were lax about guns in general. I would agree if we were only talking about should arms and handguns. They could not care less about your personal armaments when the real power lay in shipboard artillery, air supremacy, armor, and masses of ground troops. Cannons, though, would cause them a bit of concern. Enough to not want them in the hands of those they consider politically suspect.
*One's a librarian, one's a spy, together they fight communists! Coming to ABC in 1982!