Is it fraternization to go shooting with an NCO after getting off work (shift work) to practice shooting a pistol?

Your NCO was trying to avoid a perception. That perception could cause problems equal to actual fraternization. If you went and shot as a squad or fire team, that would be different.

It's not specifically listed as fraternization, but could be viewed as such, especially if the NCO is in your direct chain of command. Chances are the NCO was just avoiding any and all chances of having the situation appear like fraternization. Just like it's not cheating on your wife to go have a beer with another lady after work, it might be in your best interest to avoid that question altogether by passing on that drink.

Hunter- Fraternization is similar to Sexual harassment- it is the perception to others that has to be defended. Tho unlike the SH which is normally brought up by the 2 concerned, Fraternization can be brought up by anyone, more easily the SH.