I’ve noticed that issue with other plugins, intermittently. Which suggests it might be an issue with the WordPress plugin delete process (unless anyone else has noticed this issue with MT recently?). If refreshing the page and trying to delete the plugin again doesn’t work, I usually delete the plugin directory manually via FTP. So in this case, you would delete the microthemer directory:
/wp-content/plugins/microthemer
If you need any assistance with this, feel free to send FTP details via our secure contact form.