To reduce either character to a villain may force you to miss the nuances of each of these works.
Macbeth is your typical tragic hero, someone who has great potential and opportunities but is destined to fail on a large scale. He hopes for the throne, but wants to obtain it through the usual channels, not by murdering his way there. He is influenced by his wife, and he is limited by fate (or the Fates, represented here by the three witches). During the plot of Macbeth, he moves from a noble, decent man to one who is manipulated into horrible acts. The acts are not his idea, nor does he seem to have much of a plan other than to cover his other deeds up.
In Great Expectations, Miss Havisham may have gone through a similar rise and fall of fortune, but we don't see that during the course of the novel. She is presented as a broken character whose actions are not what breaks her; rather, her actions show how broken she may be. She manipulates Pip into his yearning for Estella.
The only real similarity I can see in their villainous actions is that their actions may be influenced by outside forces. Miss Havisham is a woman burned by a man. Her actions could be seen as revenge against all males. Macbeth is influenced by his wife, but his actions are not vengeful. Neither character fully owns their behavior, and the pity that the audience/reader feels for each of these characters is a result of our ability to see them as victims rather than truly maniacal villains.
Sorry, I don't agree with the underlying assumption that either character fits nicely into the villain stereotype. If you are analysing these characters from a more modern idea of villain, you may have more luck. The modern villain often is a result of external forces, often a product of abuse. If you must label them villains, I recommend that you focus on the pity the audience feels for these characters. Focus on the understandable origin of their horrible deeds as their deeds are very different in nature.