If you're okay with the images being on a CDN, why wouldn't you also be okay with the HTML and CSS also being on the CDN? Just fronting the entire static site with a pull-through CDN is an easy solution that doesn't require any complicated workflow.
Or do you just check in images to GitHub and call it a day?
Usually you just store the images in the same git repo as the markdown. How you initially host the static site once generated is up to you.
The problem with storing binaries in Git is when they change frequently, since that will quickly bloat the repo. But, images that are part of the website will ~never change over time, so they don't really cause problems.
Working Copy (git for iPad) handles submodules reasonably well, I have a few that I'm working on cloned on it and others are not so I don't use so much space.