Using Markdown instead of HTML is a very bad idea for several reasons:
- Markdown has no spec, so every library works differently in details. The output which you'll produce using CKEditor may give a different (even totally wrong) result when transformed to HTML by your back-end. For example - escaping image's title and link texts - you won't be able to ensure that the text user inserted does not break the output.
- Not all HTML can be transformed to Markdown.
- There are plenty of tricky cases which are totally correct in HTML, but cannot be done in Markdown.
- Markdown has fewer features than HTML, so you'd lose some content which users produced.
- You actually gain nothing by using Markdown instead of HTML.
I am a CKEditor core developer, so I know it very well. I tried to implement a Markdown writer for CKEditor and very quickly I found that it's completely pointless. I don't say that it's not possible, because it is, but only a limited stability can be achieved - too low for anything I would personally want to use in production.