It might be a dirty solution, but what you could try, is let the microflow trigger a java action to carry out the actual delete in the background (community commons, RunMicroflowASync/InBackground) and log out the user after triggering that java action.
Or use the Queue module (or the Mx9 equivalent) and set up a job that deletes the account with a delay, so you have time to logout the user.
If users still run into the error, mark the account as ready to delete and log the user out., block ready to delete accounts from logging in (in your Home flow perhaps) and clean out any ready to delete accounts every hour or so.