Give it time.
You bring up an interesting point in terms of the gods, lesser gods, demi-gods, and humans. Tolkien has more or less "cleaned up" all that mess. Or has he? I did read somewhere (Shippey's Greatest Author of 20th Century?) that Tolkien was, in part, in
The Sil, attempting to do justice to that strange half-mythical bit in Genesis 6 where it talks about the sons of gods and daughters of men. If that is part of what Tolkien was about, it seems strange to me that the two lines of the Children of Eru are what he came up with.
As for "Dark Ages", from the Renaissance until the early 1800s, the entire period from the Fall of Rome until the Renaissance, were considered the Dark Ages. Then certain persons discovered that the Cathedrals had not sprung from the ground as miracles of God, but had actually been built by those very same people that they had until then believed to be hopelessly ignorant imbeciles, lost in the midst of the Dark Ages; lo and behold, they had actually built the cathedrals. The opinion of the medievals shot up in the 19th century. Since then the term "Dark Ages" has been reserved for the period between the Fall of Rome and roughly 1000, which was the close of the onslaughts of Vikings from the north, Muslims from the south, and Bulgars from the east.
So the Thirty Years' War, being after the Renaissance, was considered an Early Modern tragedy (atrocity?) that stemmed from the Religious Wars of the Reformation.
You do make an interesting point in regard to how the Free Peoples are all rather "free of stain". They are an exception as far as humans go in Middle Earth, however; there were the Varangians, Easterlings, and Haradrim, all who had been at one time or another, enslaved by Morgoth or one of his servants. That which rendered the Free Peoples (at least the Human variety) as relatively "free of stain" was contact with either the Elves, or with Numenoreans (who themselves had been heavily influenced by Elves).
In place of Religious Wars Tolkien sets up the Dark Lords and their minions versus the Free Peoples. How much similarity, however, is there, between the struggles of early Europe against Viking, Muslim, and Bulgar, ... and ... the struggles of Arnor against Sauron's minions?
So I'm not quite convinced that Tolkien had such a romantic view of history. I think it might be more accurate to say that Tolkien used what is known about history to create his feigned history, necessarily altering things to fit his Dark Lord versus Free Peoples set-up.