This may already be an open request and if I missed it I apologize. We need the ability to unmanage a component within an application template....From what I can tell you can unmanage the entire template but not just a component.
For right now we have to either leave the component in a down state or remove and re-add at a later date which is less than ideal.
Thank you for your feedback mdriskell. This actually has been requested previously. We're currently tracking this feature internally as FB28909.