How do judges align the incentives of a law clerks with the Judge's goals?

By choosing like-minded clerks:

Supreme Court Justices solve the principal/agent problem by tending to hire law clerks who generally agree with their bosses’ views of the law. That agreement gives the Justices more confidence that their law clerks will be faithful agents without the Justices having to engage in costly monitoring of law clerk performance.

By choosing clerks with the same judicial philosophy, you reduce the inherent incentive conflict between the principal (the judge), and his agent (the clerk).