That'll drive them to use encrypted channels without oversight. The functioning of many a government agency isn't a derivation of the official processes. The official processes and record keeping are something that needs to be "Worked around" in many of these agencies.
The foundation of America as a country was based upon the Founding Fathers deep mistrust of the concentration of power. They used the word "Government" to describe this back then, but today, the influence of governmental agencies, private corporations and large unions with outsize decision making powers all threaten regularly the exercise of individual liberty as this case shows.
The answer is to return power to the people. The default scenario shouldn't be that someone gets arrested for whatever reason an unelected bureaucrat decides. Government or their agencies should have to request express permission to breach an individuals liberties and not the rubber stamp BS they follow now with warrants that require a threshold that's more likely than not to be granted on a mere suspicion. Transparency in this process is much more key to the honest functioning of Government than many others.
Much too often, for the sake of brevity or to just follow a routine, judges and the people entrusted with safeguarding these liberties and acting as a check tend to obfuscate much of the process or worse, leave it up without the possibility of contesting the decision until after severe actions such as remand are carried out. We need to reinforce individual liberties.