Actually, three of the Eastern Air Temple's pagodas were set on fire, causing it major damages. Upon Guru Pathik's arrival, however, most of the temple was restored. The point of the genocide was to destroy the Air Nomads, not necessarily everything about them. This is why the temples were kept untouched, apart from the Eastern Air Temple, as the point was to kill the Air Nomads. Given the fact that the firebenders had one day to destroy airbenders from all four temples, burning the temples would be a waste of time, rather than directly attacking their target.