Disable the native Twitter embeds introduced in WordPress 3.4.
If you saved a post containing a Twitter embed before activating this plugin, you simply need to re-save it to make it go away.
In most cases this should be unnecessary, since Markdown ignores existing HTML. But if Markdown for some reason disturbs your HTML when making an edit to a non-Markdown post, either check the "Disable Markdown formatting" checkbox, or put a
<!--no-markdown--> HTML comment in your post somewhere (useful when using a mobile or 3rd party blogging app).