| Yes. Ministry certainly has the blade out for Christianity here, but I believe that The Book of Revelations in the song is really Aleister Crowley's The Book of Lies.
Robert Anton Wilson devoted a good bit of attention to its Chapter 69 in his Cosmic Trigger. He claims that the verse, and "Frater Perdurabo"'s commentary on it (which I'll spare you) leave little doubt that the rutty old goat is talking about mutual oral sex, with swallowing. Get it? "69"? "Suck seed"? (nudge nudge, wink wink).Wilson decided that this kind of sex magick was the Secret of the OTO.
I suspect that Wilson, Crowley, and Ministry were all guilty of some form of self-abuse.
The Book of Lies - LIBER CCCXXXIII
69
ΚΕΦΑΛΗ ΞΘ*
THE WAY TO SUCCEED -- AND THE WAY TO SUCK EGGS!
This is the Holy Hexagram.
Plunge from the height, O God, and interlock with Man!
Plunge from the height, O Man, and interlock with Beast!
The Red Triangle is the descending tongue of grace; the Blue Triangle is the ascending tongue of prayer.
This Interchange, the Double Gift of Tongues, the Word of Double Power -- ABRAHADABRA! -- is the sign of the GREAT WORK, for the GREAT WORK is accomplished in Silence. And behold, is not that Word equal to Cheth, that is Cancer, whose Sigil is (69)◊?
♋ / ♋
This Work also eats up itself, accomplishes its own end, nourishes the worker, leaves no seed, is perfect in itself.
Little children, love one another!
Notes:
*The Greek letters in the title are Kappa-Epsilon-Phi-Alpha-Lambda-Eta Xi-Theta. Don't ask me.
◊ The (69) in the verse should actually be the astrological symbol for "Cancer", which looks kind of like 69 lying on its side. | 
