You can upload images to any album, whether it was created with Lightroom or Backlight, via the Backlight Publisher. Those images uploaded will not be manageable from Lightroom. But since you want to ditch Lightroom, this shouldn’t matter.
There is no setting to separate Backlight from Lightroom. I think you just simply stop using Lightroom to manage the albums.
If you stop using Lightroom to manage your albums and sets, you can still manage them with Backlight.
To test this, create a new test album via Lightroom. You can set it to be hidden under the Features tab.
Upload an image via Backlight Publisher. Try deleting images initially uploaded via Lightroom Publisher.
If you want to be assured that your albums will still be on the site even if you uninstall Lightroom, try this:
Create a new Publisher instance in Lightroom to upload to your current site. Add a few albums. Then delete the Publisher instance in Lightroom. Lightroom will ask if you want to leave the images on the server. Click on Yes.
Your albums should still be on the site and manageable through Backlight Publisher.