I usually get rid of @EnableAutoConfiguration and then selectively import the auto-configuration classes I actually want with @ImportAutoConfiguration.
A Spring developer once mentioned, on a mailing list post i have long since lost, that the autoconfiguration stuff is pretty much demo-ware. It's good for getting a simple app up and running fast, but for anything serious, you should import the configurations manually, exactly as you say. Fortunately, that's an easy enough transition to make at any point in a project's lifetime.