The end of Waterdeep!
Outstanding!
Some interesting elements to consider:
1) The powerful casters of the Watchful Order of Magists & Protectors, Danillo's Bard School, and the Harpers, up to and including Maskar Wands, Laeral, and Khelben himself.
2) The guilds. I know it doesn't sound like much, but what influence and power due they wield with the almighty gold piece? None want a significant disruption in trade...unless of course they were behind it all along.
3) The Churches. Not only would they take unkindly to a 'Bane-led' force, they would have significant resources both inside and outside of the city.
4) Force Grey, the elite protectors of the city from powerful adventuring types. Also very likely to succeed at a mission like killing an army's powerful leader.
5) Halaster, newly appointed chosen of Mystra, and the forces of Undermountain.
6) The denizens of Skullport. Friends or foe? Should anarchy erupt above, what would this bode for those below? Do ancient pacts of support exist between the leaders of these two cities for mutual protection.
7) Alliances. The alliance of Lurien (under Alustriel's rule) and the Knights of the Shield (North), the trade alliance.
8) Powerful magical defenses including the 50' (epic) golems (that's plural), a walled city, atop a plateau, with a heavily fortified castle, atop an embankment, all supported by a significant air cavalry (griffon riders) and naval fleet.
9) Numbers. During it's peak season, Waterdeep is said to boast nearly 1,000,000 in population. That is an enormous number of people in a fantasy world.
Given the above, I didn't get the impression you were pulling a "Shark" on them, and dropping some 50th level Epic Demon Cleric that rode it's pet Force Dragon at the lead of his very own army of 50,000 vampire troll barbarians. (Yeah, baby!) Instead, you've got a powerful cleric leading a powerful army on a fortified stronghold. Under the circumstances, I would recommend (instead of an outright "sacking" of the city) that you instead chase off the travelers, merchants, mercenaries, and visitors, which knocks their population down to about 200,000 - 300,000, a far more manageable number. Most of the old city is in ruins. Those alive have held up in one of several key strongholds throughout the city (Castle Waterdeep, Khelben's Tower, The churches, or perhaps even in Undermountain or Skullport).
And then comes the counter-attack! Just in time for the PC's arrival.