This is a discussion I've had more than once myself: essentially it's science zombies vs magic zombies.
I like to make some of the same distinctions, especially that the virus-created "zombies" are easier to kill, since magic can animate something even when it's down to just a skeleton and a virus is still subject to the laws of biology and physics. (that line in the Resident Evil movies about how zombies can go forever with no food just killed me, but now apparently they've moved on to the virus granting magic-psycic powers, so why are we even trying to justify the realism? but whatever)
The balance that I usually put on the magic zombies (since they are tougher, and usually benefit from either intelligent directions or a hive-mind mentality) is that magical animations are not "fire and forget" spells; they require continuous magical upkeep.
This means that either the necromancer has a cap on the number of zombies he can raise (unlike a virus which can spread unchecked) or an uncapped magic spell might eventually make so many zombies that it drains the life right out of the necromancer, killing him, at which point the magic-zombies fall apart relatively quickly. If the necromancer is already undead, then it drains his negative energy, redeadening him.
Now excuse my while I go check the thesaurus for different words for "dead", so we can get past all this dead/undead/dead-dead/redead junk.