He may actually have been AFRAID at the last minute she might miraculously rise up and say, "Hey, mom and dad, Mikey BEAT me up." And maybe that her body would not decay and show signs of a martyr. Lots of killers are very obsessive and nervous about getting rid of bodies, even doing REALLY nutty things during the process of disposing of the body. It's psychological. They want the evidence gone and the image of the body gone from their memory.
At the very least Schiavo has a problem with power and authority, having a need to control everything having to do with Terri.