I think here you are also somewhat proving the point because you can "go HTML", since the problem is more about markdown not kicking in. I'm mostly kidding but since we are talking about "blogs" (mostly pictures and text) it's OK for there to be a bit of jank. Remember, this is a script for you! You do not have to justify the jank to anyone!
Seriously though, I think that what you're describing is a real failing of Markdown. I wanted at one point to use Restructured Text but really you want Sphinx and Sphinx is not meant to be used as a library unfortunately.
The problem is that part of the time it won’t kick in when you want it to, and part of the time it will kick in when you don’t want it to. I’ve seen plenty of examples of both.
I have a well-established track record of disliking Markdown because of how grossly technically unsound it is. I’m steadily designing a more principled replacement for at least my own use, drawing most significantly from reStructuredText, AsciiDoc and Markdown.
Seriously though, I think that what you're describing is a real failing of Markdown. I wanted at one point to use Restructured Text but really you want Sphinx and Sphinx is not meant to be used as a library unfortunately.