While it is certainly possible to see John Brown in both ways, I am more inclined to see him as a murderer than as a martyr. Fanaticism is not typically justified, even in a good cause.
John Brown was clearly motivated by a good cause. Slavery was one of the worst injustices to ever be perpetrated in relatively modern history. It certainly needed to be destroyed. However, it is not at all clear that the people who supported slavery deserved to be killed out of hand.
Yes, slavery was evil. However, it was also something that was accepted by millions of people at that time. Let us imagine that one day we come to believe that abortion is a clear evil just as we now believe slavery was. It would still not be valid for someone to go around murdering people who support abortion rights today. That is essentially what Brown did. He took it upon himself to kill, and to try to kill, people who were on the other side of what was then a political and moral divide with people on both sides. This is the work of a murderer in my mind, regardless of the fact that I celebrate his cause and think that the people who owned slaves were guilty of a great evil.