Easiest way of deleting users from Cisco Unity is from the SA. Check out this defect for details if you run into problems when you re-import them (there are a some known issues).
CSCec74329
NOTE:
What version of Cisco Unity do you have? Based on the version you have there could be an Engineering Special(s) that can be applied to address your problem with MWIs. Also check out this defect:
CSCeb20635