I was going down the same road as you in my thinking LW. I think what I will do is differentiate between active and inert corpses. And all the necro spells that raise undead will specify that an active corpse must be used. That way the transform should be enough.
Let me know what you think of this too. I was thinking about making the transform (both ways) cumulative and that they either have to overcome the body of the corpse or the points used to transform it, whichever is higher. So if a Priest takes the time to work his magic on a body and builds to say 20 points of transform, even though the corpse only had 10 body, if a necromancer wants to overcome that with an opposite spell, it must beat 20 points rather than the 10 in the corpse itself? Obviously this would be a rare case since most casters are not going to take the time to just do this willy nilly for every corpse they find (or make). But for the occasions for when they want to make the effort, it can be done.
Also thinking about creating items that they can make and place in an area that have an area affect suppression of necromantic magic intended to raise undead so that if they want they COULD make a graveyard more resistant to being used by a necromancer. Thoughts appreciated.