I just quit DEVONthink, opened Terminal and pasted defaults write com.devon-technologies.thinkpro2 RenderMarkdown -bool FALSE. Selecting a Markdown document after relaunching opened in Edit mode, not rendered.
What OS and version of DEVONthink are you running?
Independent of the preference setting issue, what do you exactly mean by “could no longer edit the MD file”? Generally, you have to toggle the “text alternative / best alternative” icon in the toolbar right above the preview pane to switch between rendered and editable mode. Are you not aware of that procedure, or are you saying that in your installation this toggling does not work?