Hi Alan,
The autoconfig-users-freepbx.sh script is there for you to modify and do whatever you want. You do not need to keep it untouched, you can modify it so it extract users, password and permissions from somewhere else.
The next release is around the corner (have to add one more feature, write docs, package and release), you can download the beta right now, together with the freepbx module that lets you manage users, permissions, groups, etc. The fop2.cfg on the beta has new features, keeping backwards compatibility in format, but is not exactly the same, as there are new permissions and as a new features the option to define group and assign groups to users. The new config options are described here:
View Post 209&p=813&hilit=fop2admin+1.0.tgz#p813