All of the characters in the Matrix blew shit up to remake the world in their image. Does that make them villains? Same argument could be made with the Boondock Saints as well.
With regards to Marla, it definitely seems like Tyler wanted to kill her. But Tyler's motives were always very conflicted because they were actually Narrator's motives all along. Perhaps the Tyler personality only wanted to kill her so that he could drive the Narrator personality to the breaking point where he could take control again. Tyler always did seem keen on training and educating Jack.
