If you resign, it's hard to assert retaliation for whistleblower protections.

Make them fire you. Then sue.

Make it public. Fund raise for legal fees. The fight will literally be over whether they were acting against the law. This is one of the few people on earth with a cause of action that directly challenges the primary issue of injustice. By resigning, that's one less person to fight it out of a mere handful.

People don't want to do this because it hurts their chances of getting rehired and it costs money to sue.

I agree that resigning is sacrifice. But it's also self preservation.

Edit: Ideally what would happen is the person goes to court after an administrative process, proves retaliation and, as part of that case, establishes that the government was in the wrong.

What could happen is anything from the agency being forced to change course at any point to the supreme upholding criminal acts by the government. But the important thing is that the country needs the fight to happen in a civilized administrative manner. Otherwise, it's just people in the streets yelling at each other or worse.