I understand your reasoning, but anti-aliasing means removing jagged edges, thus while MLAA and similar techniques may not be considered true traditional anti-aliasing techniques, they do remove jagged edges.
That’s not exactly true. You can use per-sample shading in the light-prepass step and then per-sample fetches in the material step (actually, you can use per-sample shading here too, though it would be an overkill). This way it should be working as expected, I think.