A military dictatorship was a form of government run by the military, with no input from the citizenry. The Klingon Empire was a prime example of this form of government.
While destroying a military dictatorship was not always possible, organized resistance could produce favorable results; history offered many examples of this. In 2267, James T. Kirk and Spock detonated a munitions dump outside Kor's headquarters. Later, the captain explained that he had done it to prove a point, encouraging the Organian Council of Elders to sabotage their Klingon occupiers even if they couldn't mount a full-scale war against them just yet. (TOS: "Errand of Mercy")
In 2372, hearing of Admiral Leyton's plan to depose Federation President Jaresh-Inyo and set up a Starfleet-run government instead, Benjamin Sisko asked him if he really thought that other Federation worlds would just sit back and let their legitimately-elected president be replaced by a military dictatorship. Leyton scoffed at the idea, though Sisko explained how his coup would cause a civil war. (DS9: "Paradise Lost")