I know that my players would immediately and irrevocably decide that anyone who slew a whole village is EVIL through and through, even if the villagers would subsequently have died in another way. They'd be in no doubt that gaining power by killing is evil, and they'd act accordingly. As Wednesday Boy says, I wouldn't worry about that. And I wouldn't worry about tons of background working itself into the PCs' hands. If they do research, present them with written results, so they can read and refer back to it.
Just recently my PCs went on a long quest to recover the bones of a Saint, because he was important to them and it seemed fun. They have been presented with info several times indicating that this saint was not as saintly as he is now being portrayed, 400 years after his death. In the long run, they didn't care. They recovered the bones, woke an evil pirate's ghost ship, and took the bones to the Temple, which will be putting them on display to their followers.
I knew TONS of backstory about exactly the motivations of each NPC and faction in the campaign; people here helped me create some of it! But the PCs only knew that they'd been hired to get the bones, their hirer was actually ambivalent about the project, and eventually discovered that in the ancient past, their hirer's ancestors actually were the ones who arranged the Saint's assassination (and he was their KIN). Afterwards, the two PCs who were FROM the region decided they'd best leave and stay gone for a few years while the ramifications blew over, so as not to be accused of fomenting civil unrest. The PCs had a chance to read lengthy diary entries by one of the Saint's followers; they instead read the bullet point list I provided, and ignored the rest. Oh, well...
A lot of times, knowledge of what's "really" going on just helps you make the actions of various parties seem authentic; not simple, not failing to confuse an onlooker, but true to the world.
The PCs may never know why the NPC is killing villagers; if they do, they may not let it weigh with them; if they do, then they'll look for other info to back up their beliefs, most likely. And that's when they can find, for example, a letter written by the villain's true love to her mother bewailing the changes in her beloved "ever since... event x...". That's how I handle things, anyway.