There is a big difference, most "freedom fighters" target military and government (authority targets), terrorists target innocent civilians. My own father was executed as a "terrorist", but he never targeted innocent civilians.
But isn't the problem here significantly more troubling than simply making the freedom fighter/terrorist distinction? The men killed in Yemem were suspected terrorist. Who decided their guilt/responsiblity for what act of terrorism?
Do we rely upon an adminstration headed by Bush, Ashcroft, Rumsfield who see a terrorist under every turban?