Well, much of the evil is truly evil. But there is the recurring danger that good people become seduced by the evil, and the acknowledgement that the capability to be overcome by that seduction exists in "good" people. I'm not sure that I see the dichotomy as a ruling idea here.
I'd agree. The truly evil characters are barely present in the books; the stories are much more about how the rest of the world reacts to the threat.
Saruman, Denethor, Boromir, Theoden, the elves choosing to largely stay out of the war...these are people facing hard decisions with limited information and no expectation that victory is possible.
How many of us would make choices in the face of the end of the world that an outside observer would call unambiguously good and wise?
Denethor is actually a great example, who also happened to be done a fair amount of disservice in the movies.
In the books, Denethor is a rational character who is recognized for his wisdom and insight. Gandalf has immense respect for him (though they are not friendly) and at some level they are peers - not at a fundamental level, obviously, Gandalf being Maia.
Denethor is the character who is using reason to get through the day. He isn't operating on faith like Gandalf. He's used the palantir, out of necessity, so he understands the situation better than anyone else. He's stood up to Sauron himself in one-on-one mental battle time and again. He thinks, quite rightly, that Gandalf's plan to send the Ring into Mordor is insane: if the Enemy gets the Ring, everything is over. The most rational thing to do is to hide the Ring away in the most secure place possible (Minas Tirith), and, in the event that they have no other choice, to use the Ring to defeat Sauron. Of course, he accepts that that choice is already out of their hands. Frodo is already gone.
But Denethor has known, all this time, that Gondor (and therefore the West) cannot hope to defeat Sauron. They are ultimately doomed. Gandalf affirms this even after Denethor dies, when he proposes the march to Mordor. Even after their victory at Pelennor, they are doomed. They have defeated only a tiny fraction of Sauron's forces. The last straw for Denethor, of course, is losing both his sons on top of knowing they are all doomed (after a last consultation with Sauron.) But when you look at Denethor through this lens, he looks a lot different than his portrayal as a crazy madman. What distinguishes him and Gandalf is Gandalf's faith that everything will work out.
