As David Reynolds said of John Brown's "Provisional Constitution", we could say of Brown's militant Christianity: it was "hardly unproblematic".
But it's also useful to look a bit more closely at how Brown's religion translated into his social outlook. Obviously, between the 9/11 attack, car bombers in Iraq, subway bombers in Spain and Britain, suicide bombers blowing up restaurant patrons in Jerusalem, and more more of the like, the whole notion of violent action in pursuit of religious convictions is "hardly unproblematic" for us today.
However, though Brown himself was strongly motivated by his own Christian convictions and his sense of a religious mission to help abolish slavery, his movement was not a religious movement. It was a movement to free the slaves. He didn't fight to drive out Methodists or Mormons. He fought to end the "peculiar institution" that made the lords of the lash owners of their fellow human beings.
It's common, and deeply misleading, to generalize about religious fanaticism. While religious people fanaticial and otherwise may share certain characteristics, they also have forms and customs particular to that religion. Reynolds addresses the inevitable comparison of Brown with you-know-who and makes an important point about Brown's religiosity:
Brown had a breadth of vision that modern terrorists lack. He was an American terrorist in the amplest sense of the word. He was every bit as religious as Osama bin Laden - but was the Muslim bin Laden able to enlist Christians, atheists, or Jews among his followers? The Calvinistic Brown, reflecting the religious toleration of his nation, counted Jews, liberal Christians, spiritualists, and agnostics among his most devoted soldiers. Bin Laden's ultimate goal was the creation of a Muslim theocracy in which opposing views, especially Western ones, were banned. Brown's goal was a democratic society that assigned full rights to all, irrespective of religion, race, or gender. (my emphasis)
Whatever similarities John Brown's democratic Christian militancy may have with that of present-day radical Muslim Salafists like Bin Laden, the goals toward which they aimed as well as their methods were radically different. If the effect of their actions in the real world of human society is a measure, any meaningful comparison would be difficult.
W.E.B. DuBois also gives a sense of the variety of followers Brown assembled in preparation for the Harpers Ferry mission:
These were the men - idealists, dreamers, soldiers and avengers, varying from the silent and thoughtful to the quick and impulsive ; from the cold and bitter to the ignorant and faithful. They believed in God, in spirits, in fate, in liberty. To them the world was a wild, young unregulated thing, and they were born to set it right. It was a veritable band of crusaders, and while it had much of weakness and extravagance, it had nothing nasty or unclean. On the whole, they were an unusual set of men. Anne Brown who lived with them said : "Taking them all together, I think they would compare well [she is speaking of manners, etc.] with the same number of men in any station of life I have ever met."
They were not men of culture or great education, although Kagi had had a fair schooling. They were intellectually bold and inquiring - several had been attracted by the then rampant Spiritualism; nearly all were skeptical of the world's social conventions. They had been trained mostly in the rough school of frontier life, had faced death many times, and were eager, curious and restless. Some of them were musical, others dabbled in verse. Their broadest common ground of sympathy lay in the personality of John Brown - him they revered and loved. Through him they had come to hate slavery, and for him and for what he believed, they were willing to risk their lives. They themselves had convictions on slavery and other matters, but John Brown narrowed down their dreaming to one intense deed. (Dubois; 286-7)
Reynolds also gives us a glimpse of Brown's Harpers Ferry band at the same time:
Accustomed to wilderness camps, the men didn't mind the hard lifestyle. They divided their time between military preparation - which included studying Forbes's Patriotic Volunteer [a military manual], readying rifles, and making belts and holsters - and desultory activity such as chatting, singing, and playing cards or checkers. They sang hymns like "Nearer My God to Thee" and sentimental ditties like "Faded Flowers" and "All the Old Folks Are Gone" (they changed it to "All the Dear Ones Are Gone").
They debated religion and other topics. Stevens had a copy of Thomas Paine's Age of Reason that he passed around for others to read. John Brown, tolerant as usual, encouraged the group to discuss Paine's skeptical ideas, even though they conflicted sharply with his unwavering Calvinism. The men kept up with the news by reading the Baltimore Sun, which Brown had subscribed to, and the newspapers and magazines that Kagi sent in bundles from Chambersburg. (Reynolds; 298)
Paine's Age of Reason was a strongly-stated argument, heavily influeced by his personal involvement with the French Revolution, that was highly controversial when it was first published, earning him accusations of atheism (which were true). But it was a militantly skeptical book in religious matters.
Within his family, apparently none of his children (he had 20, of whom 12 survived into adulthood) carried on the intensity of Brown's devotion to the Christian God. Brown was very concerned over the spiritual health of his children's souls, and tried always to convince them to follow the ways of the Lord. Yet their lack of faith, and even open skepticism, didn't seem to affect the intensity of his love for them.
In other words, Brown was more concerned in practice with the deeds of his followers and family than with their professed religious beliefs. Obviously, he had far more in common with a Jew or a Spiritualist than with a Southern minister of the Gospel who endorsed slavery.
I'm not sure it sounds consistent to say that a devout Calvinist like Brown, who believed in predestination, respected freedom of the conscience. But, in practice, he obviously did when it came to matters of religious faith. And he was clearly a man who was not afraid of ideas. He had no fear that "dangerous" ideas from Tom Paine would harm him, or his followers - at least no such fear that he would hide from such ideas or expect other to do so. I'm sure he found much in the professional revolutionary Tom Paine to admire, apart from his religious skepticism.
Brown was convinced of his faith in an other-worldly God. But he saw it as his mission to serve that God in the fight for the freedom of the slaves and the defense of democracy here in this world.
(See Sources on John Brown for references.)
An Index to Confederate "Heritage" Month 2006 postings is available.