OMG. Here’s hoping this post will save others hours as well.
Yes, you must remove the wp-engine code from your mu-plugins directory. AS WELL – you must remove the mu-plugins.php file itself. This file is not something required by WordPress and in fact contains the calls to the wp-engine code. (Technically, you could just remove the mu-plugins.php file and you’ll be fine since the mu-plugins structure is such that WordPress doesn’t read in sub-directories like it does in plugins.)
