>Of course innocent until proven guilty applies but the justice department knows that and still brought charges. At the very least, they believe they've proven beyond a reasonable doubt his guilt.
It's a bit of a nitpick, but the Justice Department (DoJ) hasn't proven anything.
The defendants in question have been charged (and arrested?), but no trial (or plea bargain) has been held. As such, presumably the DoJ has what they believe is sufficient evidence to convict the defendants on the charges brought against them.
However, until a trial (or a plea agreement) is concluded, the DoJ hasn't "proven" anything. Rather, they brought charges against some folks. That's not "proven beyond a reasonable doubt," that's making accusations and bringing the case into the court system.
What the DoJ believes (and/or believes it can prove) is not proof in and of itself.