Cantor's is only one way of looking at sets and containment. And even it, from a point of view like Goedel-Bernays-VonNeuman set theory this result only declares that the class of all sets is not a set, not that it does not exist. Variants of this solution provide models of mathematics that allow for a set of all sets (or at least a class of al classes, or a category of all categories), but they must sacrifice either some applications of negation or severely limit the degree to which self-reference makes sense in order to evade paradoxes like Russell's.
From the viewpoint of someone like Descartes, contradictions do not controvert omniscience. Instead, the fact that we cannot handle this apparent contradiction merely demonstrates the limitations imposed on our thinking by our nature as temporal, human animals -- including the very notion of contradiction. Applying this notion to mathematics (though through a Kantian lens) Brouwer decided negation is probably an aspect only of temporal thought, based entirely on our notion of before and after in time, and that we should not trust it completely: we should either limit it to finite cases or retain its temporal character.