I don't know of a way to get around this and actually I hope there isn't a way because that would mean that QlikView isn't that secure.
All I can say is that it is important to save a backup of your QV application without section access before developing section access. When you have a stable version with section access then you can delete the backup that isn't secure.
Also, in my experience, section access can be really sensitive to things that don't matter when you import normal data into QlikView. For example, I would load the ACCESS column before the USERID column and I don't think * in NTNAME column is going to work.