Really, that is the point. The network was created under the ownership of an Organization vDC. It belongs to it and is shared from it. For an Org vDC to be deleted, you have to remove all content inside of it first.
This is just how the product works.
You figured out a workaround, which is what I would typically suggest. If you have many Org vDCs in an Organization, don't share. Make an Network per Org vDC which is not shared. You can follow this path, but it does have some additional configuration overhead. It does prevent some scenarios like you did experience.