I believe the reason they were able to step in our private affairs was because it dealt with interstate commerce. The consitution is clear that the feds have that authority. So I have no issue with that case.
I havent seen anything which says those intrusions can, backed by the Consitution, otherwise interfere with private dealings. Now sure the government is wont to pass laws saying it can do whatever it wants. But that doesnt mean it's ok, or superceded our rights.
The ruling seems to come down to the following: "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". And that's because wheat was traded nationally, so even though the event was local the effect was national on the market. Guns arent traded on a national scale. The price of a glock in GA has no impact on the price of a glock in NY.
Further an individual sale of a privately owned gun doesnt impact production, it was already made. Consumption, guns generally arent consumed or used up, at least if it's being sold. Or marketing.