I am unsure how quickly they move. Flamethrowers could be used to push them to an area. Having a ground vehicle drive over a concentrated area would work. As would having a number of ships turn on when there are many around - they could be sucked into engines. Though, that may damage ships.
And then there are explosions, as I mentioned.
If we could evacuate Knowhere, we could also poison the area and return once it's dissipated.
There are many ideas. I am certain my sister would also have theories I have not yet considered.