Remove iAPP without removing components

Interesting idea. You can change an iApp from managed control to manual control, but the iApp still exists. What you want is the option to use the iApp for "deployment" only and not "management", which would have to be a new feature request.

The big problem here, from a design point of view, is you know people are going to use that feature and then want to delete everything the iApp created (for one reason or another), but not have an easy way to do so since it has all become disassociated.

Anyway, your best option is to open an enhancement request with support.