I've used it for that, and the inclusion of HTML is sometimes a nice "escape hatch": you can write pages mostly in Markdown, but include inline HTML when you need to add formatting or interaction to a page that Markdown's own syntax doesn't support.
Some Markdown parsers have an option to sanitize embedded HTML, e.g. Discount, and its bindings in various languages, does a very basic s/</\</g when the "no html" option is used: http://www.pell.portland.or.us/~orc/Code/discount/
