"We exist only to serve."

The Bene Gesserit is a secret sisterhood in FrankHerbert's novel Dune.  They train their bodies and minds over years of conditioning, giving them physical and mental powers on the verge of superhuman.  Outsiders often refer to them as 'witches'.  The Bene Gesserit play a large, though secretive, role in the running of the empire.

The Bene Gesserit primary agenda is a gene manipulation program to generate the Kwisatz Haderach, a male Bene Gesserit with the psychic ability to look within their own soul in ways that female Bene Gesserits cannot.

Paul Atreides turned out to be the Kwisatz Haderach a generation earlier than expected, and he had powers beyond what the Bene Gesserit expected. Exactly what were the Bene Gesserit expecting?

And talk about twisted...they wanted Lady Jessica (Baron Harkonnen's daughter) to produce females so they could be mated with Fayd Harkonnen...and they wanted to preserve Paul Atreides gene line by having his daughter and son mate!  ''One presumes since this was a controlled process that the usual genetic reasons against incest were non-existent.  As to the morality issue, yeah, it's bad, but the Bene Gesserit weren't exactly goody-two shoes when it came to morality in general.'' [I'm sure they found themselves to be behaving completely morally; you can't hold them to some fictious absolute :)]
* They were breeding humans for particular traits. If doing so is moral in the first place, then the particular case of inbreeding is just normal practice; see the history of livestock/dog/cat/etc breeding. So the question isn't whether they were immoral because of the incest issue, the question comes a step before that; is breeding humans moral?

Yes. Incest is a probate means to strengthen any (positive as well as negative) characteristics in a gene pool.

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See also the novels of RobertHeinlein - not a lot of relevance to the BeneGesserit, though. If you mean relevant to a discussion of morality, then move to another page?