It worked for Begins because that was two different characters. But here it's just one character who turns out to be Brainiac. For people who don't know Brainiac such a reveal is meaningless.
Keep in mind that the vast majority of the audience for a superhero film will consist of people who don't read the comics or watch the cartoons. Plenty of people who saw Batman Begins
had never heard of Ra's al Ghul before, but the reveal still worked for them, because Ra's was established and defined as a character early in the film. The key would simply be to make the reveal effective in a way that didn't depend on name recognition. They could've handled Brainiac the same way Nolan handled Ra's, by having a scene early in the film where Superman learned of a dangerous Kryptonian AI named Brainiac (perhaps while browsing the Fortress's database, similarly to how he learned of the Phantom Zone villains in Superman II
). Or they could've had the surprise of the revelation depend, not on who
Brainiac was, but on what
he was -- the fact that this supposedly heroic Kryptonian was actually a murderous AI would be perfectly effective as a surprise revelation regardless of the AI's name recognition.