A Court of Owls for Superman

[Doctor Know]

They basically did this way back in the late 80s with the Millennium storyline. The Manhunters were in Smallville (and stuff).

Sure, it was basically universe-wide, but there was a lot of weird stuff going on Smallville because of it.

Apologies, somehow I didn't see you had already posted this.

Great minds think alike. The Millennium event ended up being a cluster with the New Guardians. But all the the stories woven to build up the event were cool. Those devious Manhunters.

[Vordan]

Just take JMS' approach from Supreme Power

Jonathan and Martha were government operatives chosen to raise Kal-El. The residents of Smallville were observers.

Hell, even Lois was recruited by her father to keep the alien under control.

Perry has been in on it from the day Clark was hired. It's why the Clark Kent disguise worked- everyone was in on it.

Adding to what everyone else has said, that would make for one hell of an Elseworld.