The government's motion [1], as the article quotes, says that it "does not anticipate arguing—as Defendants claims—that Defendants 'specifically used an encrypted messaging application to evade law enforcement'". They concede that this would be irrelevant under the particular statute at issue. Instead, they argue that banning any mention of encryption is too much. They pose a couple of reasonable-sounding hypotheticals for when the encryption might be relevant. For example, "if Defendants attempt to attack the thoroughness of the Government’s investigation, the Government may need to present evidence that its investigatory avenues were limited by Defendants’ use of encrypted messaging." The article flippantly dismisses these without justification.
The judge's ruling [2] took the obvious middle path between the parties: the government can't bring up encryption as evidence of guild. If one of their hypotheticals actually happens during trial, they can approach the bench and ask to admit it then. This seems eminently reasonable to me.
[0] https://www.courtlistener.com/docket/63007873/united-states-...
[1] https://storage.courtlistener.com/recap/gov.uscourts.med.615...
[2]https://storage.courtlistener.com/recap/gov.uscourts.med.615...