Strictly speaking, from an etymological standpoint, there is no reason to suppose "commemorate" should imply either a positive or negative connotation of what is being remembered. That said, it feels a bit weird to say, "We commemorate the Holocaust on Yom HaShoah," because it seems that "commemorate" is in fact slightly marked to imply memoration of a positive event.
(1) Is "commemorate" in fact value-neutral? In any case, is it best used in collocation with positive events?
(Ideally, please provide citations from high-quality writing to support a liberal position on this.)
(2) What would be a better word to use with a bad event?