In some ways it is a fair point. The law is set up to provide many protections for individuals.
It reminds me of when they threatened Flynn that they (was it the FBI back then?) would pursue his son unless he cooperated. You get this sense that no one matters as much as pursuing the investigation.
Nevertheless, it's also the nature of the beast, when there's another, possibly higher, purpose, which is to respond to a claim that all Americans have been damaged by Russian interference in US democracy. Finding out if the president colluded with Russia is worth the price of some broken eggs.
So yes, the judge has made a true observation. But also, Mueller is bound to behave this way to defend the Republic. And the judge really has to accept that.