It's easy for others to say, "oy, you coward, you should have blown the whistle" from the comfort their web browsers. For what it's worth, I had a security clearance in a previous job (not as high as yours, I'm sure) and I understand where you are coming from. I would have likely done the same as you. Especially with my career and the ability to provide for my family on the line.

It's probably different if you have a family, but I have quit jobs over moral implications no problem. Most people have pretty flimsy morals and will do anything to keep the money rolling in.

The mistake wasn't in not blowing the whistle but it was taking a job with this kind of organization in the first place.

Yeah the solution is to not put yourself into a position where you need to make these choices. The fuel for the fire that are organizations like the CIA are people who don't have moral qualms or who have flexible ones.

The less people who work for these organizations the better.