The 2nd amendment is indeed therefore a protective safeguard against someone in the government taking us over with military power, transforming us from a republic/democracy into a totalitarian regime.
This is a weaker claim than your previous version, which said that without the 2nd Amendment the US
would become a totalitarian state. Based on the actual history of democracies, though, this claim is also wrong.
If you look at cases in recent history where democracies have been transformed into authoritarian states, you will find a common pattern. Rather than the military simply stepping in and overthrowing the legitimate government, what's happened is that broadly popular authoritarian movements have come into power, often by democratic means, and then undermined or eliminated democracy and freedom. This was true across a broad swathe of Europe after World War I (including most notably the Fascists in Italy and the Nazis and Germany, but also multiple other authoritarian movements), it was true of the Peronists in Argentina, and it's true of the governments of Poland, Hungary and Turkey today.
These authoritarian movements have been characterized by extreme nationalism, xenophobia, contempt for democratic norms and any kind of "weakness", and embrace of the need for a strong leader. To the extent that armed citizens outside the government played any role in the loss of democracy in most of these cases, it was to
support the authoritarians as paramilitary units.
The same kind of anti-democratic, authoritarian impulse exists in the United States, and is currently embodied in Donald Trump and his supporters. The same nationalism, xenophobia and scapegoating, the contempt for "losers" and embrace of "strength", the undermining of democratic norms -- the whole authoritarian package(*). Those who are most likely to share this vision of the US -- rightwing Republicans -- also happen to be those most likely to be heavily armed. If authoritarianism really does come to the US in the foreseeable future, it will be supported by armed citizens, not opposed.
(*) Though fortunately with a leader who lacks the drive and the discipline to be really effective.