Maybe Sin was at some other part of the planet or just didnt kill as many people to begin with. Because it does say somewhere in FFX that each Sin was stronger then the previous one since it is made of the aeon that defeated the sin before it. Maybe the first was not that strong. Zanarkand had just spent numerous years in war and was on the brink of defeat when Yu Yevon created the first sin. This means that the city was probably not in that great of shape due to shortages in supplies and the city was also probably bombarded during the war destorying and weakening structures in the city. So it was easy for the first weaker sin to show up, destory the city, while never using an attack anywhere near as powerful as the sin made from Braska's final summon. The first sin may have been more of a pain in the butt then any real threat, maybe just sinking a ship here blowing a building over there and so on. After 600 years of this Gandorf final decided to end it and destroyed the first sin. Unknown to him sin would be reborn and be stronger then before. The stronger sin brought a much quicker reaction, although still a hundred plus years, because it was capable of killing and destroying more. So each time sin was destroyed and reborn it brought quicker reaction due to it being stronger, until it reached the strength of the final sin.
Just my thoughts anyway.