Encrypting it and securing it very well at a technology level means that the human element (I'd argue) becomes the easiest way to get access to it - i.e. someone with sysadmin access, DB access, or just working on a project where the APIs and/or tools available can produce valuable information. This is true even if the 'player' (with system access) has to be 'recruited' by the attacking or defending team some time after taking up the job.
Couple this with the fact that even the security agencies themselves are prone to corruption, malfeasance, human error, (no-one is perfect), and insiders, and you could easily end up with a confusing mess. Bear in mind that everyone wants their agents to operate and be able to communicate back without detection, again regardless of which team.
Compartmentalization must also come into conflict with inter-agency sharing rules -- at some level, people need to know what is going on and make decisions -- and trust must be a big issue for many of these groups - they probably spend a ton of time watching themselves and others, and watching for information leaks / canaries / spread of misinformation.
I'm certain there'll be some fascinating stories eventually from all of this - it all continues to make me believe that concentration of power and information (which I think are continuing as a trend) only end up in creating dangerous situations, and that decentralization is ultimately the preferable way to go (in that it prevents a small number of people from having too much power/influence/control, and equally protects those same people from being targets themselves).
I'd find it hard to believe that there are people that don't fit that profile but are moles for governmental intelligence agencies even exist.
Real spooks don't carry a conscience, they'll exploit anything they can to get their grubby hands on the data they need.
"For all you know, some 20-something long-haired unix
hotshot could have been busted for drugs at some point and
"repurposed" as a mole in exchange for leniency."
Excellent point. Previous comment retracted.
Even without that, trusting companies because their employees are honest is hard.
There are some people at the NSA who really really care about privacy and not spying on US Citizens and believed we didn't do so. In fact, most of the ones I've met. However, with sufficient compartmentalization, they don't know what they or others are truly doing. Same can be true for any company.
Are you working on Google's data liberation system to not trap users in your system or are you working on NSA's data exfiltration system for Google's data. I's not always clear.