Calm down. 
This issue is very specific, it’s not about being unable to deactivate “GAPPS”.
This only concerns the Google App, not “Google apps” in general (like Hangouts, Drive etc.).
Android 6 has a new feature called Assist. The Google App is set as the default Assist app. If you disable the Google App, you have to set the Assist app to None or you will end up in a boot loop. You only have to do this once.
Since this setting does not exist in Android 5, you have to make sure the Google App is enabled before you upgrade. After the upgrade you can disable it again, set the Assist app to None and you’re good.
This is not specific to Fairphone, it’s a well known issue. But I agree that the Updater should at least warn you about that.