When someone tells you about "the Greater Good", it's time to worry.
I'm almost drawn to the thought that, just as evil doesn't really exist as such, although there are evil acts, the same can be said of "good". Good for whom, is always a good (
) question to ask when presented with something said to be "good". (Being somewhat sentimental, though, I still cling onto the thought that there is real good out there.)
I think some of this has been rehearsed in the Goodkind Wizard Rules thread (whatever it's called). Good isn't good just because someone says it is.
What your characters (and you, as the author) are left with is a more complex scenario, as The Curious Orange has suggested. It is up to you how much of this you show in your story.
Personally, I think a really good antagonist for your hero is one with depth, one who may cut corners, may ignore the feelings and rights (including that of life) of others, but who, in their own mind at least, is out to achieve something "good". An out and out mindless sadist is usually dull, beyond the invention (you the author) put into their cruel acts.