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If the machines don't want the humans to rebel, then why don't they just smush them when they come out of the pink goo things? And why do the machines want to rebuild Zion after they've destroyed it with 23 people?

Well IMO the machines just can't controle everybody that much to know who wakes up and where.Plus by letting them fall in the water (or whatever that was) they die anyway because they are not strong enough to swim (unless they are picked up, obviously).
They rebuild zion because they need it. They need to have the non-believers removed from the Matrix an the only way to do that is with crews like Morpheous crew!