I like the idea of tornadoes and maybe destroying buildings outside too and the eruptions would be a nice touch too. It would be cool if you took different actions for different disasters like flooding you get to the highest elevation you can or dig down for tornadoes and eruption burns anything wood.
Destroying terrain is probably a no-no at this point. Same with destroying constructed tiles. The ramifications of a destroyed tile are vast. This also makes earthquakes and tunneling invaders extremely problematic.
If it is handled as a weather event that moves creatures around, but only moves creatures around, then you can have dwarves blown off of a cliff or pushed against a wall for injuries. I'd also imagine loose items could be blown around as well, so you could have socks flying around at high speed and they could potentially cause damage.
As far as flooding, there is already code in the game to generate 1/7 liquid upon impact with a raindrop, but this 1/7 liquid only spawns when a rain drop hits a pond tile. If raindrops could spawn 1/7 liquid anywhere, and a rain storm was kept up for some time, including even months, then you could get some serious flooding. Same deal with lava. A nearby volcano could present in fortress mode as a rain of lava, creating a 1/7 unit of lava wherever it hits on the surface.