Possible way to legally discipline a wayward President

Through the militia.  However, while Congress does have powers associated with that, what is conspicuously absent is the role of the President.

From the US Constitution, Article I, Section 8:

To provide for calling forth the Militia to execute the Laws of the Union, suppress Insurrections and repel Invasions;

To provide for organizing, arming, and disciplining, the Militia, and for governing such Part of them as may be employed in the Service of the United States, reserving to the States respectively, the Appointment of the Officers, and the Authority of training the Militia according to the discipline prescribed by Congress;

Alas, the President is mentioned later, Art II, Section 2:

The President shall be Commander in Chief of the Army and Navy of the United States, and of the Militia of the several States, when called into the actual Service of the United States; 

Question:  What if the Congress is controlled by Republicans, both House and Senate, and decide to call forth the militia?  Let's say that instead of a law, which must be signed, they issue a joint resolution to that effect.  The States appoint the Officers, not the President.

Ok, then the President decides that he doesn't like what's going on and he issues an order for the militia to desist from whatever they are doing, and the militias refuse.  Then what?

Let's say the militias were "repelling an invasion" of illegals from the border and the President says he doesn't like that, and wants it stopped.

What can the President do if the militias, Congress, and several states decide not to obey him?

I got the idea from reading a post and watching a video on Barnhardt.  No, she doesn't advocate something like this exactly.  She merely points out how a genocide was stopped by a militia.

If a President is trying to flood the country with illegals, the Congress and the people are not helpless in the face of it.  Of course, the GOP must actually try to do something like this in order to stop it, which is altogether a different question.

Update:

It looks like there's a legal way to do this through the State Defense Force, which is authorized by Federal Law.  The respective State Defense Forces are mostly inactive.  By law, the Governor of each state is the commanding officer and the forces are mostly independent from the Fed.  The President is still commander in chief, so a political conflict that became quite serious could eventually become something of a crisis.   Nevertheless, this does water down the authority of the President, in which there is no easy remedy for him.

The question is whether or not there is a political will to oppose this president.  That has always been the case.  There's no excuse along the lines of "our hands are tied".  No they are not.