The peaceful check & balance would be for the Executive Branch to stands up against the others and refuse to oppress the citizens.
True. The executive branch can choose not to enforce stupid laws. In your OP, they have apparently made the decision to do so however.
If it goes beyond that, the next check and balance won't be so peaceful. They want my guns, they'll have to come take them.
But 51% of the people aren't supposed to be able to strip the rights of the 49%.
Also true. Rights are actually suppose to protect the minority. In your OP, the loss right effected everyone. Another one of those 99% situations.
We'd have more guns and more liberty.
Certainly a better world than the "Just Following Orders" outcome.
Let's try an analogy on this situation. 2nd Amendment "...the right of the people to keep and bear Arms, shall not be infringed." There have been several cases before SCOTUS on this subject, the results basically allow reasonable regulation. It can easily be argued that regulation is infringement.
In Indiana we must have this little pink card to carry a handgun. Perhaps this is infringement and a violation of rights. Ironically, those who ignore this are considered criminal and those who comply with this ingringement are considered proper.
While we may disagree, we do not openly defy this regulation. Many of us are in fact involved in having the requirement removed. So the point is, we work through the system to change what we think is not right.