Well Pre retcon MM did (when he was angry IMO) slag billions of universes but a Omniverse is infinite more and Merlyn has fused all the life energy of the Omniverse into crystals that he can break at the same time with basically a thought so I think he is the One of the two that can destroy the omniverse fastest.
Rebuild it would be MM, be repaired all the damage Beyonder and him caused, with a wave of his finger. And Merlyn hasn't really shown any Rebuilding feats According to my knowlegde.
Molecule Man for the win here IMO.