Old thread, but to summarize:
This ~~strikethrough~~ style is specific to the GitHub Flavored version of Markdown. It is not part of Markdown proper, and not part of MultiMarkdown.
If you want to use it, use “GitHub Markdown” as the syntax highlighting for your drafts (selectable by draft, and can be set as the default for new drafts), and use change your Markdown Settings to use GitHub Markdown instead of MultiMarkdown.