First things first, I worked on editing the BoT and the web enhancement, so my views may not be completely objective.
Cheiromancer, in re-reading the description, I see your point. Nothing is stated explicitly about what is so wrong with them. I read the description as the necrovores being an unintended consequence of experimentation, intended to create creatures which would be able to slay undead. Instead, we have creatures who consume undead. I would guess one of the things "terribly wrong" with the necrovore is that it consumes undead in the first place - a creature that lives to feed on undead flesh creeps me out as much as an undead creature feeding on living flesh. Certainly, any civilized creature turned into a necrovore would be tormented by its new nature, probably also becoming an outcast from its former society. Though the template doesn't specify an alignment change, one is certainly possible, especially with a base creature of good alignment.
BTW, while reading the description, it occurred to me that the template doesn't change the ability scores of the base creature, meaning an intelligent base creature becomes an intelligent necrovore. What do you suppose would happen to say, a hill giant, which has been perverted in this way? Most townships aren't going to appreciate having this thing hanging around their graveyards, so it can't be sure of its next meal, and a hill giant probably needs a lot of provender. One solution is for the hill giant to establish a working relationship with a mad wizard or necromancer. The hill giant necrovore provides protection, captives for experiments, and so on, and the wizard provides free meals. Everyone wins - except, of course, for the locals. If the party doesn't realize that they're dealing with more than a simple giant, they could be in for quite a surprise, given the necrovore's immunities (plus the buffing spells the wizard could cast on it).
Another possibility is for a very powerful creature turned into a necrovore to use its new-found abilities to dominate other undead, using them as its minions, consuming a few every now and then. I could easily see a yuan-ti cleric necrovore with the Death domain running a powerful group, with possibly even a vampire in its service. Of course, if the vampire only serves out of fear, it might provide clues for the pc's, hoping they'll take out the necrovore. The vampire then flees, the party thinks they've solved the problem, and the vampire returns later, when things have calmed down, to take over the necrovore's minions. Set this in the sewers of a large city and it could take the players a long time to catch on.
Just a couple ideas I had...
