Personally, I can't see the Voodoo Lady being evil. She may have a lot to do with the constant battle between Guybrush and LeChuck, but I have a feelings here intentions would be pure. Something about keeping a balance of things or something. I'd love to know which parts of the story in ToMI were Ron's idea, and wether he managed to sneak in a couple of elements to lead the developers of the next game on the right track. If the Voodoo lady thing was his idea, I wouldn't be surprised if this would have happened in Ron's MI3.
Of course, Ron loved to mess with people's heads (as shown in the ending of MI2), so the Voodoo Lady could very well have been the main villain all the time, surprising both Guybrush and LeChuck in his final game with her ingenius plan to merge future and past into one bubble within the Bermuda triangle, hence a slow trickle of modern devices into the pirate world.