Is the FBI themselves going to be comfortable using devices which, say, the Chinese government, has the source code & keys for? The NSA and CIA certainly won't be. This is a two way street and they damned well know it.
Now the Chinese and every other country in the world can prepare and sign updates to most anyones iPhone, say the FBI directors iPhone.. Heck, if he's travelling in China it would likely even be trivial to push the update over the air to his phone...
The FBI having the ability to break in to NSA or DOJ machines is definitely not ok and I'm not sure anyone is going to say otherwise besides the FBI. Hell, we can't even trust the FBI agents with a few bitcoins.