I shot Maurice for exactly the same reasons. The choice was never an option of being good or bad, it was the games way of asking if you would adhere to its storytelling and continue Aiden's characterisation as a merciless bastard or make a choice he never would. Of course I shot him, because that's the only thing Aiden would have ever done. There was no choice, just an illusion of one, and picking anything else would have been lying to myself.
Aiden is a criminal who's painted as a hero by bad writing. I would have liked Watch Dogs a lot more if they fully embraced his criminality but they try to brush it under the rug even when it's shooting you directly in the face. Nothing is ever his fault except it always is. Everything bad that ever happens to anyone he loves is a direct result of his actions, but the game never makes him accept his role in any of it. The narrative would have been infinitely more interesting if it ever did.