Good news: This has been fixed in 2.1.0 Enterprise BETA, and will ship with our 2.1.0 Enterprise release (and subsequently merged back into HEAD for those checking out nightly builds).
Now, if you delete either the XML or any one of its renditions, the delete confirmation dialog asks you whether you want to delete the current item and all associated ones. Your options are either to delete or not delete - just like with submit, they always go as a set.
We are also looking into enabling move and rename and adding similar behavior, but those two will more than likely be part of a subsequent 2.x release.
Kevin