When there are competing legal interests (First Amendment v. need for a fair trial) the courts generally balance these two interests.
One way is to make sure the gag order is no broader than necessary. (That's why the DOJ is careful to ask for a "narrowly defined" gag order.)
Another is to see if there is an alternate way to protect the integrity of the trial (like using jury selection techniques to make sure to screen out jurors who can't be unbiased.