But would I get a completely inactive status by disabling either or both references to BGLmanx.dll or Couatl.exe in the appropriate XML files?
Yes, you can do that (in addition of turning it off in the Scenery Library) and will make the scenery entirely inactive.
However, keep in mind anything else from FSDT or other developers using the Addon Manager (QW, Flightbeam) will also stop working so, maybe, it's just easier to uninstall the scenery with its uninstaller, which will automatically care of removing everything related to that scenery, but only that.