Wasn't there some medicine you can take with which you can survive a emission?
Otherwise this would be a good time to cheat, it's always funny that the other inhabitants of the zone never had to run for cover for a blowout.

An important thing to keep in mind with blowouts is that the place your GPS points you to isn't the only place you can go to stay safe. Generally any area that's enclosed enough will protect you, and the GPS will just point you to the closest of these locations, but if you run in a different direction and end up closer to another such location then the GPS marker should change to the now closer one. So just try to remember where another nearby building, tunnel, or cave is, then run like hell for it.

You don't need to take cover in the factory. Your GPS just marks that location because it is the closest safe spot to you.
Try the opposite side of the bridge - you should be able to find cover in the Ranger Station. Noah's Barge in the swamp is pretty close, too.

edit - I'm too slow :P

Another option in case you do decide to go with the water treatment plant (that's what the factory-like building is). When a blowout strikes, the mercenaries who camp over there gather into one room and won't pay much attention to what's going on outside. Once the NPCs have left their positions outside, look for a pipe opening on the right, there's also a manhole nearby (adding a screenshot showing both entrances).

Btw, the fact that NPCs leave their post and head into designated shelter during blowout can be exploited to gain access to other areas as well :)

1) presumably you're on about CoP?
2) the building you're on about has a relevant quest tied to it