This is the impression I have thus far. I have been to the Plano sets (my pics were used on the front page of this site) and watched filming from afar in a number of Chicago locations. I have no real support for this theory, though (just being honest), but my guess is that Zod et al. do reveal themselves first, whether intentionally or not, and manage to convince the government that there is an alien living among us who has not revealed himself (Supes). Clark is not yet Superman. Zod and the government begin looking for him, find evidence of his ship in Smallville, and the game is on.
Zod's motives are always to rule, but as Shannon has revealed in interviews, it's not always black-and-white. It was not just Supe's planet that was destroyed - Zod's was, too. And it was planet he spent a lifetime defending.
Now he's on earth, and whether he wants to rule for power or simply to prevent the planet from destroying itself, he wants to rule. If Shannon's take is right, a cool angle could be that Zod does not have any faith in a populace's ability to make good decisions. The old adage: a person is smart, people are not.
In some ways, Zod's right. Planets get destroyed because people make bad decisions. He's smarter, better, faster, stronger, experienced, and without a home.
Clark has a choice now: he's here, he's been hiding, and he discovers his identity. Now what.
Most of this is guesswork except for the parts I got from the guy on set yesterday.