Try him in a Federal Court, find him guilty and sentance him.
John Brown's crime was to attack a Federal arsenal, seize Federal property, open fire on Federal troops, and kill or wound both Federal troops and civilians. It was a crime against the US Government and no less an act of insurrection than the secession of the Southern Sates.
The reaction of the Republican Party - which was accused of orchestrating the raid by Southerners - was to condemn the raid as the actions of one man, a madman, but then also to condone it by stating that the cause that led Brown to attempt his insurrection was righteous - the cause of liberating the slaves.
There was no widespread outrage for this blatent act of insurrection against the United States throughout the North. If anything Brown's raid evoked equal measures sympathy and apathy from the northern people but once he was tried, found guilty and sentanced in a Virginian court of law he was cannonized by much of the north, turned into some abolitionist saint, which was really helpful in soothing the growning tensions splitting the nation.
Had James Buchanan acted promptly and brought Brown before a Federal Court of Law, had him tried at a national rather than state level, found him guilty and sentenced him then the issue would only have been a blip on the radar of inter-state relations and he would be forgotten and dismissed as a madman.
Brown set out to raise the slaves in armed rebellion against the Southern States and the lawfully recognized government of the United States of America and having been caught he deliberately set out to make himself a martyr. By its inaction following his capture the Federal Government allowed him to become recognized as a martyr and not just some fanatic who should have been condemned as a traitor and forgotten.