Alexander's main concern with this heavy rainfall was not necessarily the flooding of the city. If the water can rise, it can also fall.
Thus even if the roads and houses got water clogged, it would cause a bit of problem for the people, but eventually all this would subside on its own.
Hence what seemed truly dangerous to Alexander was the potential loss of his strategic grain reserves and other stocks in the warehouses during the time.
He did not want to wake up the next morning to suddenly find the water had smashed through all the warehouses and washed away all his hard earned grain and other finished export products. That would be bad on so many levels.
Hence he had close to 2,500 men deployed to solely protect those critical resources.
Alongside this concern, Alexander's main secondary worry was the sudden spread of unforeseen fires across the city.