Yeah, I've got that much. Destroyed every component on the frigate, but it still obstinately escapes at the 12 second mark. I've made sure to get the generators (well practiced from Mugaar Ice Field and Aeten Defense) and the engines. I've been playing the space missions since game launch, and this is frustrating.
To all the people who are having trouble with just getting through the missions alive, learn the routes first; the missions aren't hard for the enemies so much as the obstacles.
Your best bet in that case is just to sweep randomly all over frigate trying to get missile lock. There is that one part in front of frigates that is more durable than others, and it'll often get covered in smoke once ship turns away from you.