Exactly this.
People took it that "greater threat" had to be Doomsday or some physical beast of the sort, but I always thought that Lex fits that description well... a genius with wealth, power and resources he has, being an amoral psychopath at that... I don't see much bigger threat for the world than that.
And I do hope he'll manage to get away. I hope that Trinity and Lois will figure out his scheme and what sort of man he is by the end of the film, but won't be able to prove it, as he was intelligent enough to cover his tracks well. Add to that a good public reception he has, he should be basically untouchable.