I’ve merged your query into a nearly identical thread that already contains a fair amount of discussion on the matter. You could scroll from the top, and here is a direct link to my answer, which goes over several options.
Ultimately, the fundamental thing being missed here is that Scrivener is a hybrid Markdown editing platform, it would thus not by nature destroy Markdown you are importing; that would make its purpose with it next to useless.
Here is a thread that I recommend for those getting into Scrivener from a Markdown angle. There is a bit of a culture clash, because Scrivener was one of the first programs to adopt Markdown way, way back in the day. Almost every single Markdown-based program has gone in a different direction than it did, toward plain-text or coding style text editing where the text is formatted dynamically or in a sidebar. Scrivener’s approach is fairly unique, perhaps entirely unique (I’ve never encountered anything like it), and it can be uniquely powerful in that role.
But if you want to use it this way, you’ll want to put aside preconceptions from other editors. It’s attacking this way of writing and working from a very different angle.
Or not, some people just use Markdown because they had to and don’t really care for the approach. That’s fine too, although I cannot fathom writing in rich text on purpose when I’m in something that can do “better”. 
I speak to one of the better techniques of going down the narrow and complicated path of darkness, into word processing realms, in the post above.