"It seems likely that language such as Romans 13 would have been inserted into the Bible by the Roman authorities in the first century as a means to legitimate their own authority rather than by a just God."
lol, so now the Romans need to be thrown into the conspiratorial bag of those penning the documents. I find the whole 'it seems likely' line of argument, in the mouths of skeptics, to basically mean 'I can say any absurd thing I like and it is more likely to be true than whatever a Christian might say." This particular instance is completely at odds with both liberal and conservative scholarship. However, it is right at home with the X-Files brand of thinking.
"This mean that, among other governments, the governments of Adolf Hitler, a Christian gone bad, and Josef Stalin, an atheist, were instituted by God. But why would God institute governments that murder millions of innocent people?"
This, on the other hand, is a fair point and a legitimate challenge, and certainly one that Christians themselves struggle with. I don't have time to go into it right now, but let me submit three separate 'readings' that might help flesh out this notion in a more concrete way.
First, Corrie Ten Boom's "The Hiding Place." The Ten Boom family were Christians during WW2 who deliberately lied, cheated, and stole from the German authorities to save dozens if not hundreds of Jews. How does a very homely and innocent Christian girl come to use such techiques in light of Romans 13? She ends up the sole survivor from her family. They were all caught and thrown into a concentration camp. I strongly suggest this work.
Secondly, Dietrich Bonhoeffer. I could submit a number of works here, so I leave it to yoru research to find the right ones (I don't have time this second to give you the list). Though possessing strongly pacifistic tendencies- or at least, swimming in a circle of such tendencies- he eventually chose not to go to America when he could and instead sought to face the crisis in Germany alongside fellow Christians. Eventually, he helped in the plot to assasinate Hitler, and when that failed, he was among those rounded up and sent to a concentration camp (others, of course, were executed immediately). He was executed by special order only a few weeks (or days, I don't recall) before his camp was liberated. Apparently, Hitler really didn't want to risk his freedom. I strongly suggest his relevant works.
Thirdly, Richard Wurmbrand: in particular "Tortured for Christ." Wurmbrand was a Christian in Romania while it was occupied by the Communists. He became a pastor, and along with many others, was repeatedly arrested for his activities (not all insurrectionist... many simply pastoral duties we take for granted today) and tortured. The goal of the tortures were to try to get the Christians to renounce Christianity. Wurmbrand would eventually be 'ransomed' by friends in the West, and testified in Congress. You may recall that there was a time when people really couldn't believe that the Communists were doing naughty things- how could they? people are by nature good, right?- and he showed otherwise by stripping to the waist, during the hearing, and identifying how he received each of his many scars. He was about to take his pants off and show the rest when the Congressional members said that they believed him for God's sake. Henceforth, his organization, "Voice of the Martyrs" has been active in trying to expose human rights violations around the world as they relate to Christians, and the organization (he is dead now) does its best to get Bibles and other such things into hostile environments- in defiance of Romans 13, eh? I strongly suggest the work I mentioned and whatever else you can glean.
I submit to you that you cannot hope to possibly speak to this question unless you have interacted with these materials, and preferably done just a tad bit more research on how these folks could justifiably 'set aside' Romans 13, even from the Scriptures.
It seems likely...