Well keep in mind that judges are not experts in health stuff and can't judge things like side effects and frequency.
They are experts in law and procedure, HOPEFULLY procedures that will keep people safe, but again, that's not up to judges to sort out because it's not their area of expertise.
The judge was looking at things like illegal actions of the FDA and errors in how the drug was approved because those are the guardrails around safety, for better or worse the judge isn't qualified to say.
It's really up to Congress to change the rule if it needs to be changed. The judge is only able to say that the safety rule wasn't followed by the FDA's own admission.