The missiles hit you starting during the cast, through the end of the cast, and slightly after. What you want to do is get close to your rock and have one of the people duck in and have the 2nd person wait a quick second and then duck in. It's up to every individual raider to make sure that they are at least 5 meters from friendlies until all missiles have landed.
We tell everyone to spread out
and start heading to their rocks when the missile salvo (the one right before Defense System 3) begins.