Battle Hymn of the Republic is a song from the civil war, written by Howe to replace the profane and uninspiring songs the Union soldiers were singing. Many Christians, not just Mormons, enjoy the hymn.
Lyrics in the song ITNOG seem either 1) general or 2) about multiple cases of misled/misleading leaders and interpretting the entire song entirely about Mormons sounds pretty biased—there are plenty of suicidal cult leaders out there, Koresh at Waco for example. It could about the Crusades or about Fundamentalism Anybodies or about 9/11. Or different parts can refer to different leaders.
Anyway, the use of Battle Hymn of the Republic at the end is interesting because it feels like it is set in a minor key or at least set against minor accompaniment instead of major like the original hymn. Can someone with more musical knowledge verify this?