He is just following the law, so fight the law, no diminish the judge.
Remembering that a "single judge" following the law with authonomy launched the biggest attack on corruption of brazilian history, and the fact that he is not a supreme court justice acted in favor of an independent investigation (search "sergio moro" and "lava-jato" police investiagiont).
Which is not to say they shouldn't point out that it's ridiculous when they make their ruling, and suggest that the legislature fixes it quickly.
The Big Company (like WhatsApp, Google, Apple) is always the easy target for subpoenas, judicial orders, and National Security Letters when it comes to encrypted transmissions.
Here's an idea for a legal maneuver to take Big Company out of the picture: Suppose crypto was handled by an open source 3rd-party program that was outside of the hands of Big Company. This 3rd-party program would encrypt/decrypt all incoming and outgoing messages, and the program would be mandatory.
If you want to use WhatsApp or other Big Company apps, you must install this open source and fully vetted program. Then if Big Company gets a subpoena, they can legitimately answer that they have absolutely no control over the encryption.
I'm going light on technical details because there are many ways that this could be implemented. The main idea is to insulate Big Companies from renegade legal attacks.