I think I run the exact setup you’re talking about. I have a Jekyll site that uses Discourse for comments. But the community itself has started taking off on its own outside of the comments portion.
The folks there don’t have any qualms with getting to and from the two sites. They have links everywhere that take them where they want to go. Some of that is within the topics in the community but I think (and analytics confirm) the custom header I added helps a lot. I wanted the branding to feel the same across my sites so I customized Discourse to fit both my main Jekyll site and my tools site.
I don’t think I would worry about users moving between the two. I’ve never seen an issue with it.