It has been my experience that there is a pretty fair sized number off NCO's and Officer's in the Army that feel not only would an order to confiscate civilian firearms be illegal, but that it would cross the line to something that had to be prevented. i.e. Not just saying "No" and not doing it, but actually arming up and preventing the other folks from doing it. So Civil War 2.0 then.
This subject (or one similar to it) is a matter not only of barracks and beer discussions, but it (when exactly an order from the civilian command authority goes too far) is a repeatedly covered subject in our Professional Military Education classes. Complete with historical examples, discussions, likely outcomes, and the possibility (likelihood) of no win scenarios.
We study, and take to heart, the lessons from the purges of the Red Army and other communist purges. How exactly it would go is something I don't really want to find out, but as a professional military sworn to defend the Constitution there is an acute awareness that the Constitution and the fed.gov aren't synonymous.