Federico,
Yes they are incompatible concepts. However, one is typically treated as a subclass of the other. Its that https://www.wikidata.org/wiki/Q26869695 (nutritional diet) is a subclass of https://www.wikidata.org/wiki/Q474191 (biological needs diet) Which is correctly stated now with that 'subclass of' statement on https://www.wikidata.org/wiki/Q26869695
Yes, it looks like Wikidata did not have the nutritional concept of a Diet, but only had the biological needs concept. Thanks to your creation of the nutritional concept of a Diet, this helps everyone, Schema.org as well as dieticians, nutritionists, and other scientists.
TODO: We just need to figure out what to do with 'external subclasses' and a few other things concerning Schema.org mapping. And that's part of our Agenda on this Friday's Google Hangout with Lydia and folks.
Thanks again Federico for the bit of help!
Thad +ThadGuidry https://www.google.com/+ThadGuidry