I think two issues are being conflated here:
There’s a clear argument that the government engaged in an overzealous, vindictive prosecution here. By no stretch of the imagination were the Hammonds terrorists, yet they were prosecuted under an anti-terrorism statute. The government could have let the case end once the men had served their sentences, yet it pressed for more jail time.
I don't know the details of the case, but it wouldn't be a stretch to imagine a prosecutor over charging for a crime in an attempt to get a plea deal. If there' no plea, then the full charge goes into effect. Prosecutors can be ruthless. That said, of course the government is going to fight for the minimum sentence once the guilty verdict comes in. If a precedent is set up that a terrorist can get less than the mandatory minimum, then what's the point of having a statutory minimum? The government has fought tooth and nail over mandatory minimums in countless drug cases. That mandatory minimums exist is of questionable moral value, but as long as they're a thing, the government will fight to protect them.