Personally I regard the deadly towers as a balancing factor for the AI, since the AI doesn't adequately defend the walls. Assaults on stone-walled cities were relatively rare in antiquity because they were very costly in casualties to the attacker - sieges were far more common, starving the defenders into surrender or a suicidal sally.

Whenever I need to assault, I bring a really big army, use cheap, expendable units to take the walls and towers, and am psychlogically prepared to accept very heavy losses. That's the price I deserve to pay for wanting to take a heavily-defended city so quickly. If I don't want heavy losses, then I resign myself to a long siege.