i was thinking that because all matter somehow, somewhere has a charge, the colonies could develop a sat that, after finding a vortex, creates a magnetic field spinning in the opposite direction, thus cancelling the vortex. I only suggest this because in op2 the vortices were powerful enough to take an entire base before any evac could be done, plus, being a venus planet and all, the vortices would probably be a lot more powerful.
electrical storms(if they're included in op3) will probably be just as much of a nuisance as they were in op2, so i dont think there should be a 'defender' against those.