Akatosh is not Alduin, although they are representations of the same spirit.
They are the same being, viewed differently. The Dawn was an era of non-linear time, so when time did become linear, things had to be rectified. This is why the god of time has multiple personality disorder. Also, belief really influences the gods.
Not only that, but Akatosh is not the only spirit that created Nirn. Many lesser Aedra are stuck in Nirn and have become the Earthbones, as well as the other greater Aedra that have sacrificed their immortality.
Correction, it wasn't just Akatosh who cut pieces of himself to create Mundus. It was Shor/Shezarr/Lorkhan's creation, but used the pieces of the et'Ada, now known as the aedra (though it wasn't limited to the 8).
So it's not like Akatosh could just wipe out Nirn and rebuild it, even if he wanted to. He is probably the Greatest Aedra, and the others have a hard time existing without him, but he still can't just take apart Nirn without them. All the Aedra are a part of Nirn.
Alduin has eaten previous kalpas. Plus, it was not the god of time who created Mundus, it was Shor/Shezarr/Lorkhan who did. Plus, 2/3 god of time aspects want Mundus destroyed. It's only the relatively recently created aspect, Akatosh, that doesn't.