If we end up in a situation like in today's Cuba, there would be nothing the people can do to stop the government from doing whatever they like.

This is already the case and has been for decades. The army is far, far better equipped than a ragtag band of militia. Individuals with guns would only add to the chaos.

The individual military members are going to have quite the moral quandry about firing on its own people in a free country which was at least attempted to be built on integrity.

I agree, but also the situation you're describing is no longer a 'free country' so much as anarchy or an attempt at strong-handed rule. I'd liken it much more to the cultural revolution and the tank man.

There is already a tool for that: a General Strike. It's easier to pull off too and brings governments to their knees in weeks if not days.

How is that working out in Hong Kong?

I'm not sure why you would conflate a city-wide strike with a general strike. Maybe you could explain that part before I answer.

I mean I'm totally fine with that, though I'm led to believe this is a fairly contentious issue in American politics haha.