Hi Heather! I’m just a fellow user trying to help you here. 
I’ve been through what you’ve been through and recognize it. But what I described above is my understanding of how this feature works… and it’s by design. It’s not broken, preventing normal/typical use of discourse.
Discourse embed is a very simple, hands-off bit of functionality that’s ideal for new sites creating new content. That it can cause pain when added to sites with lots of existing content is obviously not great and I’m sorry you had a bad experience. I guess the howto topic explaining how it works (which I assume you followed) could have been improved with a warning about the risk of flooding the forum and people’s email. Muting the documentation category for your users and hiding documentation topics from your frontpage will be a big help going forward, methinks.
Meanwhile, the feature could be improved to add the functionality you describe which is a good idea! I use the wp_discourse plugin now on a site I actively manage, and I would love to be able to turn on the ability for logged in users to start new topics about content on my site, but not create all of those topics in discourse ahead of time in readiness for someone coming and wanting to reply to one of them.