I am not naive, there are problems in big organizations.
To keep the movies methaphor, the biggest fears I have come from movie like Star Wars in which the empire turns to the dark side.
I have no idea what systems are in place to prevent things like this to happen. I hope they are VERY good.
My experience as software engineer teaches me that as things become more and more complex in a system the risk of a bug increase. And opacity is a double edge sword.
Even if you have a buggy system, you do not say "Let get rid of it" without talking about the alternatives. Other thing to consider is: "full rewrites are generally a bad idea".
I would like to open this to constructive suggestions but I am afraid that without an inside view we are just shouting the breeze.