Question: why was this all kept secret if it was only with the best intentions, to keep the "good people" safe?
To avoid shitstorm. They don't want to leave people a choice. Once it's established people are not going to do as much about it. If they would announce it, there would be big time protests to stop them from using it, which would mean unnecessary trouble for them.
I wonder though. Does this stuff really surprise anyone? Everyone talking about the US spying us everywhere and I have just always thought this is the case anyway. This is what comes with using the internet and the advanced technology anyway. When it's possible to spy on people, some countries are going to do it. The British do the same as the US apparently which is absolutely no surprise when you look at the cameras in public for example. I think every stable state is doing it to a certain extend. Some don't have the technology, others might have more limits than US or GBR, but I'm sure it's happening.
I'm quite annoyed by all the people and the media going "oh my goood, they are spying on us." You must be pretty blind if you have ever thought that this is not the case.
Edit: Even funnier all the people blaming Obama for it. If I would be US president I'd run that program too I am sure. When you have the technology you don't just ignore it because of moral. You know, it's not only about spying on people and identifying terrorists, it's also about competition with China for example. If the US does not invest in such projects, their position and political importance hits ground bottom sooner than you think.
In the end prism is one of many firewalls to prevent terrorism, economic espionage and any kind of similar problems. It's how the world works today. Arms race might have decreased, but the race for superiority in telecommunications and surveillance has just begun.