What if instead of killing the story about Trask, Bureau 39, and Bessalo Blvd. warehouse of UFO of supposed Project Bluebook trophies (i.e. UFO documentation and proof), Perry let Lois and Clark write the story?
I can see this going in several directions:
1) The stuff was still there when they raid the warehouse, and they write the story.
2) The stuff isn't there, but they still write the story.
2a) Daily Planet, Perry White, Lois Lane, and Clark Kent's careers are all harmed by the article.
2b) Somehow Lois and Clark's find the proof, or their careers aren't damaged.
3) Lois takes the article elsewhere (as in Man of Steel) and publishes what really happened. What would this do to her career?
How would this one change impact the rest of canon?
This might be a good basis for a back story of Lois and Clark meeting, going their separate ways, and meeting up again later on. They both knew the truth about Bureau 39 and the warehouse, so the world turning against them (or the article ruining their careers) might create a bond between them.
