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