Eric Flint did address and acknowledge that discrepancy, in Grantville Gazette images section devoted to historical personages.
From its online copy (emphasis mine):
Armand-Jean du Plessis, Cardinal Richelieu, was effectively the ruler of France on behalf of King Louis XIII throughout most of the Thirty Years War. He was the most capable political ruler of the time, with the possible exception of Gustav Adolf. He is portrayed in the 1632 series as "the Great Villain," but that's a slanted and ultimately unfair portrait of him. In the context of the 1632 universe, it's reasonable enough, although I've taken care to give the readers as full a picture of him as possible. But in real history, he is often credited as the man who essentially "invented France" as a modern nation, and he is considered—rightly—one of the greatest figures in French history.
Most of the unsavory reputation which Richelieu has today, especially in the English-speaking world, derives from the absurdly distorted image of him given in Dumas' The Three Musketeers. The man was certainly ruthless, but no more so than any capable ruler of the time—and whenever possible, he was inclined to leave the executioner's ax lying unused. His subordinates and servants were invariably loyal to him, as was the King of France Louis XIII.
The truth is, I feel a little guilty about the way I've portrayed him in the series. I did so, simply because the logic of the plot required a really capable enemy—and Richelieu fits the bill better than anyone else at the time. But I could quite easily write a different alternate history in which Richelieu was one of the heroes.