The last step of the macro looks for the escape key to be pressed. And you can also easily stop the Keyboard Maestro engine via the menu bar icon.
Without using Applescript there’s no intelligent way of stopping the loop. The DEVONthink Applescript Suite lacks the ability to use the Readability API when converting to Markdown so I developed this alternative Keyboard Maestro approach but it is a workaround that lacks the programming sophistication of Applescript.
You can download an Applescript for managing Markdown conversion below, but the resulting Markdown is nowhere near as readable as it captures all of the HTML page elements including things like page navigation (due to the lack of the Readability API). It will however stop automatically at the end of the task without the need for user interaction.