It's been clarified but not overturned.
To expand my point for clarity:
In their own words commercial Consumption and commercial Production are both commerce. Remember, if he had used less than 11.1 acres there would have been no problem so this was significant production and significant consumption.
"Whether the subject of the regulation in question was 'production', 'consumption', or 'marketing' is, therefore, not material for purposes of deciding the question of federal power before us...[b]ut even if appellee's activity be local and though it may not be regarded as commerce, it may still, whatever its nature, be reached by Congress if it exerts a substantial economic effect on interstate commerce and this irrespective of whether such effect is what might at some earlier time have been defined as 'direct' or 'indirect.'"[4]
In other words, the fact he was Producing wheat or just Using wheat does not side step the issue. He was both a consumer and producer of wheat and thus clearly impacting the wheat market. That final bit just means picking if was a direct or indirect impact does not matter.
Now, I and others may not agree with the interpretation. But, it's not so crazy as to be a clear mistake.
Which is why I said farming wheat in such a way that it is separated from the market aka not harvesting it, would have been a useful but different argument.