There's a little area right across the missle ammo box. You can hug the walls, it will provide you a lot of cover. And when firing the missles, make sure you keep moving to avoid gunfire while guiding the missle to it's target. Remember that the gunships you fire at will first take care of the missle, but the other gunship will still fire at you.
To avoid the missles being shot down, circle the laser scope around the gunship untill the missle is behind it and then focus it on the ship, it will then hit it in the back without it being able to take it down in time. Repeat this about 5 times per gunship, and you should be home free to enter Nova Prospekt.
Also don't forget to use the containers in the middle of the square for cover.
(Yay for being the Half Life 2 guru
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