Unlike the Taliban or the Viet Cong, the US citizenry, even armed, would be like chaff.
edit: so many downvotes. I guess I hit a sore spot. I'm sorry the truth hurts, guys and gals. :)
If we descend to such a state where an American president is (a) willing to completely annihilate the population, (b) can either bypass congress or get their approval to do so, and (c) can mobilize our military to perform the annihilation, then perhaps your point is correct.
I wouldn't exactly hold my breath on that.
The VC were utterly crushed, leading the NVA to get more directly involved in the South rather than using them as a catspaw. To the extent that the combined operation had success (which it clearly did) it was because of the NVA—a regular army—and the backing they had even further up the Communist food chain.
During Tet, the VC was crushed and ceased being an effective fighting force in the south. The NVA was forced to pick up the slack.
The eventual takeover of south Vietnam was by conventional military forces.
You assume that all members of the US military would fight on behalf of the government. All members of the armed forces swear an oath to the US Constitution, not the federal government, so it's pretty much certain that a non-trivial proportion would defect from the will of the government if the orders were contrary to the oath sworn to the US Constitution. At that point, that superior training, discipline, logistics, intelligence, force projection, everything is also in the hands of the insurgency against unconstitutional orders.