Do you recall how the theory that a bacterial infection caused ulcers was rejected and then demonstrated by the doctor taking a dose of H. Pylori and developing an ulcer? He then cured the ulcer using a antibiotic that targeted H. Pylori. It was long thought that stress and stomach acid and all sorts of other things were involved. Of course, the acid and the inflammation in the stomach were attempts to kill the bacteria; they were not the "cause".
I think we are at about the same stage when it comes to atherosclerosis where wide spread inflammation of the blood vessels, adhesion of foam cells to the wall, and proliferation of cells and swelling of the vascular lining all seem to be the result of the immune system attacking a pathogen.