You must remain inside the circle for two minutes for the timer to run out. You can just run around in circles during that time if you want to. If you kill them, more will come. They only destroy your base if they can't get to you.

Your base will need defenses. I usually place my starter cabin up on a rock. The fire can go on top of the rock. Later, I dig a ditch. Stake walls are another good choice, until the blue guys come knocking.