Killing should never really be considered to be justified whether in a work of fiction or not; however, Rainsford was in a position of kill or be killed. The whole thing is a case of kill or be killed, essentially self defense. I guess it depends on how you view that type of thing, but in my opinion, if Rainsford had not killed Zaroff, then he would have undoubtedly died. Therefore, yes I believe he was justified in his decision.
As with all interpretive questions, your answer is based upon your own reading of the story and how you analyze the plot and characters. Rainsford had escaped Zaroff, and won the game. There was no reason to return to the masion and kill Zaroff except to exact revenge. Consider that Rainsford himself is a hunter, used to being in power. Although he had never considered doing something as inhumane as Zaroff in hunting humans, his choice to kill Zaroff reveals his need to be in control. In this case, his killing of Zaroff isn't about justice, but about revenge.
On the other hand, there is nothing to suggest Zaroff would have quit hunting humans. He was a static character, who didn't change even when he "lost" the hunt of Rainsford. In this reading, the audience can interpret that Rainsford is doing his part for mankind by eliminating the threat of the murderer Zaroff. After all, on this island, there is no justice system by which to prosecute him.
You will need to choose the answer that best supports your understanding of the characters.