Very fair point. I'm entirely receptive to whatever Gunn may come with, but Superman stories are always better when Lois knows, and a "Year 2" type of scenario makes that less likely.
The single best story decision Man of Steel made was to have Lois in on the secret from the beginning.
OTOH, while it's my strong preference, it's not an absolute requirement. Superman '78 remains the best adaptation of the character ever, and Lois doesn't know in that one. Lois & Clark: The New Adventures of Superman managed a delightful and romantic first season, and a decent second, with Lois still in the dark.
So I'm open to anything, depending on the execution.
If I was doing it, my take would be: She figures it out early on (say, within a week of Superman's debut), but also realizes he has a damn good reason to be using this goofy reporter alias. So she doesn't let on that she knows. (Being an army brat gives you a great poker face.) Maybe shares it with Jimmy Olsen (and swears him to secrecy), but nobody else. In the meantime, until he mans up enough to tell her himself, well... if 'Smallville's' going to be posing as a hayseed klutz towards her, she's going to be posing right back; oblivious to any romantic overtures Clark may make, but absolutely thirsting for Superman. The classic Golden/Silver Age love triangle, but this time Lois is in on the joke and it's Mr. Only-one-sort-of-girlfriend-in-high-school who's clueless.