In the GameCube version you can freeze them with a charged Ice Beam shot and then use a Missile. If you're playing Metroid Prime Trilogy a Missile won't work. You can ignore Ice Troopers if the doors are unlocked.There is a very easy way to kill Ice Troopers. First, fire a charge ice beam shot at them, then shoot a missile at them and they will shatter. This is helpful for when the Omega Pirate summons them during the battle with him.
Because of this, the Ice Troopers are by far the easiest Space Pirates to kill.