This was the way I conquered these cities in my Baktrian campaign a couple a weeks before.I guess you didn't have enough Thureophoroi or peltasts (to win the wall battle) and archers/slingers to kill the elephants from the safety of the walls.
I used 2 units of thureophoroi and 2 units of peltasts to storm simultaneously the wall from different directions and killed the Indian longbowmen, having about 30-50% casualties. When the job was done, I sent on the walls 2 units of eastern slingers and 2 units of persian archers targeting the elephants. Slingshots and flaming arrows killed some of the elephants and made the rest mad, so they started moving around killing their own men. After the elephants where gone, I sent 2-3 phalanxes and my general to kill the rest (mainly Indian spearmen). I have to mention that I play without the battle time limit.
It was a great siege battle, I really enjoyed it.
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