Cyberhank, your point about being at warp during the Enterprise encounter is correct, V'Ger was at warp until they entered the Terran system, and being so big it is possible that the Amar just wasn't fast enough. In the movie they went straight in, (we wouldnt have been able to see V'Ger's ship at all had they gone around), in the book however i dont know, i never did finish it. (and i doubt i could find it now)
Perhaps they should have cloaked and killed the power, but since we dont know how the battle was oriented, (we dont know if V'ger was facing the Klingons or not) it may not have been a possibility. Had V'ger been coming straight at them, they would have been found, powered down or not, when they crossed the cloud boundary.