Hi. I'm a huge Silver Surfer fan and have read Watchmen at least 5 times. I also understand the quantum mechanics that governs Manhattan's powers.
He is destroyed by the Silver Surfer. Manhattan has control over quantum fields from field theory. Surfer has control over the four fundamental forces of nature and wields the Power Cosmic, which allows him to do anything he imagines. He is superior to Manhattan in every single way.
Manhattan cannot control time. He once said "we're all puppets, Laurie. I'm just a puppet who can see the strings." He is a constrained along one temporal axis, just as normal humans are. Surfer is not. Surfer controls time and space to some degree. He has time traveled and taken others with him before. Surfer is superior in this aspect.
Manhattan has never been shown to destroy anything more complicated than a tank or a human. While his actual limit is much higher than shown, I HIGHLY doubt he's able to deconstruct an entity as strong as the Surfer. And even if he could, Surfer has reconstructed himself from the atomic scale.
Surfer could not permanently destroy Manhattan but he would wreck his shit every time he reappeared. Surfer has an insane speed advantage over Manhattan. That is a win for the Surfer.
As for deconstructing Galactus, that is laughable. Galactus is an abstract and only has a physicality to help lower life forms perceive him. He has destroyed abstract concepts before and wields the power to destroy and create multiverses. Manhattan is a bug to Galactus.
