The Civil War connection was not suggested to me by anyone, it's my own pure speculation, based on the date & the lamentaion, tulmult and strife of the 1st verse, not the tyrants. To me it's not simple, happy faith. For me it reads like a lot of Psalms. Sort of "I'm having all these difficulties in life, yet God is with me so I will praise Him." That's probably why it fell out of favor in the 20th cent. 17th-19th cent. hymns are full of this kind of sentiment but you find it less is the later songs.

I suspect the problem with the attribution is that no one seems to have found it earlier than 1869. Lowry may not have listed an author when he published it, but must have listed himself as the composer. This would leave it ambiguous as to if he also wrote the words or he found the words elsewhere, but did not know the author. He died in 1899 so John Julian could have been closer to the sources. OTOH, lots of stuff has been identified as mis-attributed by late scholarship. Expect for hounding on the "it's not Quaker" issue, I'll leave the hymnologists to sort that out.