If Congress, the grand jury, and the judge don't see something as an injustice, how is it the prosecutor's place to second guess them?

Every link in the chain is a chance for someone to stop injustice. If each link sees all the other links and says "eh, if it's important someone else will put a stop to it" then the system rapidly fails. (E.g., a President should not sign a law he thinks is unconstitutional because it's the SCOTUS's job to decide that.)

If we can't trust federal prosecutors with discretion because of past abuses, that's a specific and reasonable objection. But "other parties thought it was a good idea" dodges a lot. A prosecutor may be the first person available to witness how the law is being misapplied.

Good ol' superior orders.

As convincing as ever.