I plan to handle it as described in the AP. Just let players decide if they want to help, and then adjust the time required to managed depending on the number of wands.
After all it is probable that only one or two of your players can use the wands, so I think it is better to describe the event in an epic way after some RP on how they hand the wands to the church. That way the players that cannot help do not get bored looking the casters playing alone.
Plus once the wands are recovered, there is no opportunity for failure, the city will succeed anyway, so there is little reason to spend time on events players cannot impact.
That said, if you still want to play an encounter with the players using the wands to control the flood, I suggest you pick a different number of areas the NPCs are not going to defend, and let the player's choose where they are moving and in what order. Let them roll K. nature and/or K. engineering and K. local rolls to know where the water will hit next. Set a number of points for each flooding area. Make it recede will cost some charges of the wand, and other players might help constructing dikes and evacuating buildings as needed. For each K. engineering and Diplomacy check they pass, they reduce the casualties in that area until the Control weather spell is released (10 minutes). You can ask for additional Constitution checks as they go to simulate fighting against the weather, if they fail they start to get fatigated, and you reduce the number of areas they arrive on time to help or add penalties to their rolls.
That way, if the PCs perform good, the number of casualties are reduced. Then, depending where they chose to help first, some areas will have received damage whereas other not. Make people's attitude from those areas change, depending on the result of the player actions, if they saved their buildings and family or not.
The wands were stolen by Triel and Tongue Eater for their monetary value; I don't beleive they had a specific intent to flood the city. Based on that assumption, I believe you'd have to come up with an opponent or dire condition to be overcome to make this a memorable event for the players; as Balacertar states: success is inevitable once the wands are secured.
Perhaps using the rising water provides an opportunity for the morkoth to begin attacking residents and flooded buildings along Ash Avenue. Merchants along Ash would need to evacuate merchandise, providing an opportunity for attacks by the Last Laugh or Alleybashers. Either of those would provide the party an opportunity to get involved in a heroic way.