You should be fine to move the Shiro domain classes and the realm into a custom package. You might also want to move AuthController and SecurityFilters into packages, but that's probably less important.
I'm thinking of updating the quick start command to honour packages specified in the "prefix" argument. So you would be able to run:
I'll probably deprecate the name of the command and replace it with 'shiro-quickstart' too.
grails quick-start --prefix=org.example.Shiro
Version 1.1 of the plugin is on the verge of a release, but I want to try to get some more functional tests in, which requires time. I also wanted to get some proper docs done, but I guess it's better to get 1.1 out first at this point.