Whiskey Rebellion leads to Civil War

In my history 101 class today we covered Washington's second term in office. When we got to the Whiskey Rebellion my Proff said that because of the growing partisanship in the country, Washington told Hamilton that when he defeats the rebels he is supposed to give them all amnesty. Hamilton didn't neccesarily like this idea, but he agreed to it. Hamilton asked Washington if he could at least put the ring leaders of the rebellion on trial. Washington said to give them amnesty as well.

So what if after the battle Hamilton either disobeys Washington's order to give them amnesty, and instead kills them, or what if some of the men under Hamilton decided to exact execution themselves? Could this lead to a civil war in the United States? Would it be an American style civil war lead by state governments, or would it be more of an uber-rebellion style civil war? If the execution of the ring leaders wouldn't cause a civil war, what might the after effects of it be?
 
I don’t think it would be a full blown civil war, I think a lot of states would decide to leave the Union in response and at this time the Fed probably couldn’t( and maybe possibly wouldn’t) do anything about it.
 
I don't think Hamilton actually commanded any troops during the Whiskey Rebellion. He was simply a civilian advisor. The actual general in charge is going to report to his commander-in-chief, George Washington.

Furthermore, the government simply doesn't allow anyone to do whatever they want. The army/militia is not going to decide on the guilt of the men they suppress. The courts are going to (and did IOTL). Secretary of the Treasury Hamilton has no jurisdiction over the army or the courts. If President Washington wants to pardon anyone, he has the constitutional authority to do so.

Anyone who violates their orders by murdering people are going to be put on trial themselves, convicted and executed. No officer of the army is going to ignore such undiscipline. Any attempt by Hamilton to do so may cause him to be put on trial for treason as he is usurping the President's command of the army. It would also cause such a huge uproar, that it would give the emerging Democratic-Republicans a huge boost in the next election. Jefferson probably wins in 1796.

However, for all these reasons, I don't think your scenario is going to happen. Hamilton can't order them killed or stop any pardons. Militia soliders aren't simply going to massacre people for no reason.
 
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