Well, I think the main problem lies in the way the scenes are put together - had the conversion happened at an earlier point with some stuff inbetween, the Jedi Temple attack could've been more believable.

So I tend to overlook the scriptural (;) context when talking about music choice and the like - I just think it was somewhat meh and anti-climactic for the scene (and evidently so as it was c&p'd from some wacky arena scene with wisecracking heroes stabbing giant enemy crabs).
It kinda works on the level that it represents Anakin's mind at the time (not evil and hate-filled, but cold and focused, marching forward with a "what has Tobe done" attitude - and for an idealistic march theme, the piece is actually pretty dark) - but overall it's kinda lame.

Not the kind of abomination unto the LORD to me as it seems to be to you, though :)