Stopping the engine seems entirely feasible through a macro; the real issue, as you say, is starting it again. Fortunately, the solution is very easy; on a standard install where KM is located in the root Applications folder, this simple shell script will work:
open "/Applications/Keyboard Maestro.app/Contents/MacOS/Keyboard Maestro Engine.app"
It’s easy to store as a snippet in an app like Typinator and run it from Terminal or a launcher like LaunchBar or Alfred, or even to make a custom action/workflow for the latter two options. I did just that for Alfred, and showed how to do so here.