You've got exactly what I was thinking for the ones who die in KH2 -- Xemnas simply doesn't have the time to expend wiping dozens of Nobodies clean. He assumes that by the time they become really dangerous, his plans will have come to fruition. (This is also shown in Proof of Existence: the portals to the chambers of OXIII who died a year ago are destroyed, but the portals to those who died recently haven't been.)

The Samurai would be Xemnas's last, personal insult to the Nobody who gave him hope and then turned out to be not quite capable of giving him what he wanted. Roxas "died" a week after leaving OXIII, but Xemnas will force his servants into compliance for as long as he can. It wouldn't be the same if he disassembled them into Dusks first.