A young fanatic in the 1990s bombed abortion clinics in the South and assassinated a doctor who had performed abortions, then hid for years in the North Carolina wilderness from the FBI. In 2009, George Tiller was murdered in Wichita, Kansas during church, in front of his wife, by another anti-abortion terrorist.
Undoubtedly these two individuals, and those who also believe fanatically in their cause, would argue that their actions were morally justified by God, just as John Brown did. There is one key difference between Brown and these later terrorists. One defining goal of a terrorist is the desire to spread fear, to destabilize society and government. I believe these recent fanatics had that same goal, while Brown didn't necessarily. It makes neither more justified in my opinion, but the distinction is important nonetheless.
As a direct descendant of John Brown (his wife's maiden name was the same as my grandmother's maiden name), I also have to take exception with his being labeled a terrorist. Mentally unstable, perhaps, but he was strong in his beliefs, and he had the courage to risk his life in order to get his message spread outside of Kansas. This can also be said of some terrorists today, but Brown's violent acts were born from his expectation that all people be free--not from a hatred of others.