In theory, D9 would also be a useful counter to SCs, Afflictions can bring down the best of them, and the AN damage makes obscene protection SCs pretty useless. And of course magical attacks overcome "regular" etherality. Which still leaves high defense. For which F9 is superior because IIRC flaming weapons are still considered magical, and the extra attack can come in handy.
As for counters, my best bet would be anything with AOE, to make sure they can't escape it, that they die in large numbers (supposedly they should come in small numbers because they are usually harder to mass then regular units), and because its fun
Anything Evocation is usually good, I like the falling clouds of fire and of ice, thunderstrikes can work nicely, and if you can get Astral Fires against the right guys, its a lot of fun (I actually haven't been able to cast Astral Fires by any substantial amount in unmodded Dom3, only with the Sar Elad mod. Then again I haven't really tried)