These are interesting issues that would take many books or many many podcasts to cover. I will try to comment on everything while being brief. I'm not a professor, philosopher or priest, just a Joe schmoe, so take my opinions for what they are.
I recommend "Cicero Republic and Christian Arguments for Rebellion Against Tyrants". And "Christian Rebellion Theories" the latter by JM Hastings.
It is difficult to know what rebellions are justified in history in many cases. My knowledge of them is simply too perfunctory for me to say for certain. Even so, it is obvious the Christian people who took part in them thought they were. Was Heraclius justified in 610 AD? The rebellions by Copts against the Muslims that didn't succeed? The American Revolution? The Armenian Sasun Rebellion? The various Cossack uprisings against various powers, including Russia in whose service they later fought willingly?
Scotland's war for independence, Ireland's many uprisings which finally succeeded, Montenegro fights with its warrior bishops, the riots that were sometimes quite violent by Christian agitators who destroyed temples, I would say these were all justified. I recommend the writings of Corneliu Cosreanu whose entire life was one of struggle against the "legitimate" powers who were cooperating in the destruction of Orthodox Romania. He often deals with questions of how to struggle and under what circumstances.
The Old Testament is very much a part of the Bible. It is not a secondary source of literature. Christ is very much the God of the Old Testament. When Ambrose and Augustine were pushing the suppression of paganism, they were looking at the Old Testament's many descriptions of just vs unjust kings and extrapolating what Theodosius or whoever should champion. The New Testament is the record of scattered alienated communities living in a devolving Roman pagan empire. Of course it has little to say about fighting with carnal weapons. Even so, Christians did serve in the Roman military before Constantine and took part in carnal fights. The Old Testament is the story of a people and so it has a lot to say on the subject. We find ourselves now as post Christian peoples somewhere between what 1st century Christians and say Mattathias faced.
By the way it is often difficult to say in hindsight who was rebelling. Was Constantine a rebel? Well, it depended on whose side you were on. The church has always said no, but then again he won and championed our side.
More to the point--how have the jews gotten us to the point where Quaker style pacifism, considered extreme in the 17th century, has now almost become the default of even Orthodox and Catholic Christians? We have somehow become convinced that complete passivity in the face of evil actions against people who can't defend themselves is taking the high road.
I would add that civil disobedience, where it had a chance of success, is always preferable. In the modern west today I would say it has a higher chance of success by far. We don't have to start any violence to make ourselves heard, and bring about non-consensual regime change against the occupiers of our current western governments.
God bless.
