If you are using the TestFor annotation, there is already a grailsApplication variable available in the unit test you can modify that is also injected into the service. i.e.
import grails.test.mixin.TestFor
@TestFor(MyService)
class MyServiceTests {
void testMyService() {
grailsApplication.config.my.service.property = true
assert service.getMyConfigProperty()==true
}