"My Adventures With Superman" kind of did that. Waller and General Lane were hunting down Superman all while Clark and Lois were dating and at one point the General meets Clark and doesn't realize he's Superman yet Lois figured it out pretty quickly. If you wanted to go real dark, you could have General Lane hunting down Clark Kent and in the process he accidentally gets Lois killed.
I think he genuinely believe that the government hunting Superman and encountering him as Clark is kind of the same thing as the government hunting down Clark Kent as a journalist. Like, this doesn't seem like a troll.