I have no problem with the conflict as set up in the first four verses of the song (above).

My problem is that the final verse incongruously changes which side of the equation is responsible for which historical action or branch of Chrisendom.

It is the "followers of Judas" who mistakenly marry Christianity to government and institutional religion (by the auther's own admission in the first four verses). It is the followers of Jesus who would not make that mistake (in truly Christ-like belief), but would seek personal holiness and selfless living.