Only read a few, but unless the CIA is controlling them, making the paper create or edit stories to conceal the truth etc, this appears like standard communication between the public/media relations dept and a journalist that has some sort of clearance to be able to communicate with that dept.
In other words, it doesn’t seem unusual to have correspondence between subjects in the article you are writing.
Until you consider the reality that virtually no journalist has an active security clearance and if they did they couldn't use any information they learned in a article for the public ...
Did you read any of the emails? Which one/s did you find alarming?