I could be wrong, but I don’t think there’s any way to do this. Template overrides are applied by core Discourse according to namespace, not by any logic in the plugin itself.
The ‘disabled’ setting is just a setting you can apply within plugin logic to prevent it from running. I don’t (think) it can be used to prevent a plugin template overrides being picked up by core Discourse.
Actually, I kept this plugin free of template overrides for as long as possible for this reason, but the jQuery got a bit convoluted and I had to override the topic-list-item template itself.