I believe that she is neither good nor evil. Perhaps her role on earth is to maintain balance between the forces of good and evil, and must use others in order to do this. LeChuck is a very powerful evil force; his existence would throw out the balance greatly, so she needed a way of ridding the world of him, using Guybrush and Elaine in order to do so. And, by 'using them', I don't mean 'her dictating their every action as though they were puppets', I think that free will is something that she doesn't mess with, but that she merely causes a series of events and circumstances to take place in order to ensure that her will is carried out. She can probably use outside factors to cause certain things to happen - perhaps control over the weather, control over nature and animals, control over dreams, control over... physics; all of these things can potentially be used to put people in certain situations and subject them to particular circumstances. And she can also use verbal persuasion in order to convince people to carry out her will, perhaps even bribery at times
. Anyway, what I'm basically tying to say is that a) the Voodoo Lady is not good or evil, b) she is possibly a keeper of the balance between good & evil, c) she uses others to maintain this balance and carry out tasks, d) she doesn't do this by messing with free will, but does it using outside factors.