I have this problem all the time.  We are in a college community, and many employees of my clients list their home address as their permanent address.  There is a box under state tax setup that will let you ignore that state.

However, Quickbooks needs to add a feature that has WORK ADDRESS, and have the state taxes default to that state.  This is the way Quickbooks Desktop works.

I have argued this fact with your phone representatives NUMEROUS times.