The issue is confirmed on testwiki, arwiki, and cawiki. Even 'Restore all default settings' does not disable Structured discussion (the checkbox is displayed unchecked in Beta features).
Checked after deployment on wmf.17 and wmf.16 - seems to be working fine
@Trizek - some users who attempted to disable Structured Discussion beta features before the fix may have the checkbox for the option unchecked. To disable it now they may need to check it again/save, and then uncheck/save to disable it.