md2epub is a Sigil compatible script that can convert Markdown files to XHTML. The converted files can be imported inside Sigil.
Clone the repository and install the markdown dependency. Put the markdown files inside the src directory and update the sections.json file to include the files that need to be converted. I've already provided an existing template that we can readily use.
Next, simply convert the files:
$ python md2epubThe built files will be located in the build directory.