The Reverend Mother is the leader of the Bene Gesserit, a mysterious and spiritual organization deeply involved with universal politics.
The Reverend Mother is Jessica's counterpart — or foil. Both take on the role of the Great Mother, and both fulfill that role by nurturing the spiritual needs of their respective societies. But there are significant differences between the Reverend Mother and Jessica.
Whereas Jessica tends to the needs of individuals, the Reverend Mother tends to what she feels are the needs of the entire human race. This means she will sacrifice individual people if it helps the whole. In fact, the gom jabbar test she administers to Paul is used for this exact purpose: "sift[ing] people to find humans" as she puts it (1.114).
Also, Jessica's motherly loyalties lie with the people she loves, while the Reverend Mother places her motherly devotion on the mission itself. For this reason, the Reverend Mother cannot help Jessica and Paul even if the act of not doing so makes her cry (3.89-90). She cannot risk derailing the Bene Gesserit plans for creating the Kwisatz Haderach.
With that said, the Reverend Mother is also kind of in line with the witch archetype. She's oldish, she maintains an aura of mysticism, and she uses her mystic powers to bend the will of others toward her goals. Did we mention the fact that almost every man in the book refers to the Bene Gesserit as "witches"? Of course, they're just jealous they don't have awesome powers like the ladies have.
Now, you don't need to choose to read the Reverend Mother as either Jessica's foil or as the witch archetype. Feel free to use either, or both, as well as your own insights to create your own reading for this deep and mysterious character. One of the things that makes the Reverend Mother so interesting, after all, is her ambiguity. Is she a good character, or a bad character? Or is she somewhere in between, like Paul?