Just play it cautious and advance gradually with your heavier infantry/phalanxes into the city. If the elephants fight at the gates, just lob spears over the walls from a couple of akontistai units and its goodbye elephants. If they fight inside, bring your javelin boys in and keep them at hand for the eventual moment when the elephants start rolling towards your frontline infantry. Wait for them to come in nice and close and its over.

It's really just a matter of being patient and waiting for when your javelins are able to do maximum damage.