In DC Comics in the 1950s and '60s, US government agencies did not kidnap, coerce or kill. Times change. In Smallville, Watchtower has two enemies: Zod and Checkmate. There could be a three-sided war. Temporarily at least, Luthorcorp has merged with Queen Industries and is run by Oliver Queen so it is no longer a threat.
Checkmate has internal sections that are secret from each other. How does Waller know about a threat from Apokolis?