Upvote:2
I'm not sure why you're asking the question; the quotation you provide establishes that he was arrested and prosecuted - ""On July 10, 1805, Butler was found guilty of mutinous conduct." (Quote from your citation of The Writer's Response). "Found guilty" means that he was prosecuted.
More information on the trial can be found at The United States Army Versus Long Hair: the Trails of Colonel Thomas Butler, 1801-1805, which includes the following
Butler's trial took place in Frederick, Maryland, from November 21 to December 6, 1803. As counsel, the colonel employed John Hanson Thomas, a Maryland Federalist who was well connected politically and socially.21 In his defense Butler argued that hair length was a personal matter not subject to military regulation and that his delay in taking charge at Fort Adams had been unavoidable. 22 His defense won the sympathy of his fellow officers, for, while they found him guilty of disobeying the hair order, they acquitted him of the other charge.
Having been convicted of the offense, he was obliged to cut his hair; he failed to do so and was arrested again in 1804, and charged with a more serious offense. He was tried again, and convicted of disobedience of orders and mutinous conduct. Wilkinson was still not satisfied with the penalty and urged the administration to dismiss Butler from service; before the verdict was confirmed, Butler had died of yellow fever.
. . . there is little doubt that Butler went to his maker with his cherished queue intact.