Though I appreciate your response you did not resolve the question.
How can we possibly "resolve" the question, if the problem is that LM has decided to make scenery areas added with add-on.xml non-editable from the sim UI ?
Maybe if enough users would request it, they might add the ability to do so in an update. The system surely supports setting custom layer priority, just like before, but for some reason the option is not accessible using the sim UI.
Before it was simple scenery library delete then gone or control panel del. then gone. What is this new issue?
Just disabling it's even simpler now: from the Options->Add-ons menu. If you mess with the add-on.xml, you are only causing problems, because that's not where you disable them.
If you want to do it in the hard way, the file that enables/disable an add-on package is the add-on.cfg file, but that's precisely what the Options->Add-ons menu does so, there's no need to edit any file manually.
Re-arraning, instead, it's an entirely different issue, and it's made by setting the <Layer> property for each add-on.xml. It can be done, but it's best either LM will add this feature, or some smart developer would come up with a dedicate tool.