Personally I would use "so that" I think because its shorter even though only by one word and makes the sentence flow better. I think "so that" is used more commonly than "in order that" the latter seams too rigid to me personally.
If I was going to use "in order that" I would have to change it and the sentence
"Missions have to be carefully designed in order to keep astronauts safe from take-off to landing."
hope I helped :L