If you have selected the plugin’s ‘Display comments’ option, it will display comments for any posts that you have published from WordPress to Discourse. I’ll be adding a filter to the plugin early this week that can be used to control whether or not the comments template gets loaded for a specific page.
It might also be good to add an option to the plugin to not display comments from protected categories. I’m surprised this hasn’t come up before.
What is the plugin that you’re using to protect your WordPress pages?