This is the last mission of the game. Because of this, it's normal to be the hardest one. There isn't a way to give armor to Ryder or to kill the soldiers before the mission starts. However, you can collect the crates before you let Ryder in. This way, the loading process will be much faster. Also, try not to throw a crate while a Patriot or other vehicle is right behind the truck because this might harm Ryder. If you still have problems completing the mission, use Google in order to find a walkthrough or a tutorial.