I can beat this mission in my sleep, so here goes:
What you do is use the missiles to keep the Hurrim away from the shuttle. You don't need to blow them all up, just keep 'em away. In the second area, the one with the second Hurrim attack, you just have to go after the big ship (I think it's a Muurian, been a long time since I flew this mission), blow it to Sokar, and the rest of the Preybirds'll leave your shuttle alone.
PS, your kill # for Preybirds'll go through the roof after this mission if you decide to kill them all. (I did... ugh, it's like 2 squadrons out there...)