Rodney says "There is a tsunami heading towards the city." Tsunamis hundreds of feet high do not occur in open water. In open water they travel fast but are only small. They only grow only when they hit shallower water.
The wave is similar in size and destructive power to a tsunami near the shore, without actually being one. This was a hurricane wave charged by extreme wind over a much larger area than Earth can provide.
If you look closely at the trees "blowing in the storm" out the window of the gate room you can see the stage hand shaking them to create this effect.
After Kolya admits Weir is still alive, he sets Sheppard another ultimatum, threatening to kill Weir and McKay and leave Atlantis, which would then be destroyed by the storm. This threat would only be credible if the shield blocking the Stargate had been disabled. But if the shield had actually been disabled, and the Stargate could be used, then nothing would prevent the Genii from sending in even more reinforcements, this time successfully.
However, as Zora says earlier, assembling more reinforcements from the Genii would take at least another hour, where the storm would have already hit. The shield is not functional for outgoing wormholes, which makes the threat issued credible.
However, as Zora says earlier, assembling more reinforcements from the Genii would take at least another hour, where the storm would have already hit. The shield is not functional for outgoing wormholes, which makes the threat issued credible.