Because the mirror is designed to be big as possible and fit in the empenage of a 747. This isn't an ordinary 747, it is a 747SP which is a shortened version of the 747-100B capable of flying longer ranges at higher altitudes. It can cruise at altitudes up to 51,000 feet where the air is thinner. Also at those high altitudes there is little water vapor in the atmosphere to interfere with the infrared observatory.
