Hi Simon!
Both those upgrades you mentioned sound awesome. I think it would make a lot of sense to have the option to automatically not display comments from protected categories. I’m also surprised this hasn’t come up before, but I guess I’m your official canary in the coalmine. 
I’m using Patreon Plugin Pro which I’ve tweaked a little bit to work with my webcomic site.
For now, should I just disable the link in the Wordpress post?
P.S. For what it’s worth, having the comment template load on the page actually helps me a bit in this scenario, because it also automatically disables the Disqus comments on the page unless I manually input a comment in the Edit Page metabox. Not sure what will happen if the Discourse comments template doesn’t load at all for an individual page.
I suppose for me my ideal result would be to load the comments template (thus showing a live link to where to comment on my Discourse site, as well as disabling the Disqus comments) while still not showing any individual comments from the protected category.