Although Mariner is the daughter of two Starfleet officers and an ensign herself, she also distrusts authority. It’s hard to blame him for not trusting Starfleet, especially when they arrested his mother on charges she knows aren’t accurate. Here’s the thing about Starfleet, though: they’re generally extremely good at their jobs. You don’t survive very long in Starfleet without being the best of the best, as Starfleet faces every type of threat imaginable in the galaxy. If someone isn’t extremely capable, they’ll likely end up becoming Gorn food or a phaser stain before too long. This means that those tasked with investigating Captain Freeman are just as competent as the Captain herself, and they are not about to be fooled by mere executive work.
It turns out that while Captain Freeman was on trial, Starfleet conducted a secret investigation into the Pakled bombing to see if there was more to the story. They discovered that the Pakleds had edited the incriminating footage of Captain Freeman to frame him for the bombing. Apparently the Pakleds wanted to try to get Starfleet to move them to a more resource-rich planet as a reward for their crimes, but it all didn’t work out because the Pakleds are fine, Pakleds and Starfleet are the best and the brightest in the universe. .