I don't think shredding some one on the atomic level would be any less effective than turning them into a cupcake, if we are going to argue transmutation bypasses durability. Which, in this particular case, I don't really buy, given the esoteric stuff that has failed on both Juggernaut and Kuurth. I can't see Sentry turning him into anything. But transmutation involves first taking things apart and turn putting them back together. Sentry may not be skilled enough for step 2 but stopping at step 1 kills people just fine.
Basically, he's the cosmic equivalent of Scar from Fullmetal Alchemist.