How to select a service implementation in a Grails application?
It's of course possible to retrieve the reference to service from hand-built factory, but in my opinion, the approach you've taken is the best one. I use it myself, because it gathers all the information on configuration phase of the application in one place, so it's easier to track down which implementation is used.
The pitfall with autowiring that you've encountered can be explained very easily. All the classes put in grails-app/services are automatically configured by Grails as Spring singleton beans with autowiring by name. So the bean definition you've placed in grails-app/conf/resources.groovy creates another bean, but without the defaults imposed by Grails conventions.
The most straightforward solution is to put the implementation in src/groovy to avoid duplication of beans and use the following syntax to turn on the autowiring:
beans = { repository(FileRepositoryService) { bean -> bean.autowire = 'byName' }}