. They know exactly how volatile and dangerous the mutagen is, yet they choose this weapon to attempt to destroy the drones, despite the risk it poses to civilians in Underrail. Why would you put civilians at risk (the drones hideout is right next to Rail Crossing, from what I remember), when a few dreadnoughts would do the same job? And the CAU don't even manage to finish the job properly, because you will meet FD mutants afterwards, which means some survived. (Now wouldn't it be ironic if someone in the FD would end up with the same mutation as Wyatt in the junkyard?)
I can't imagine Cathcart would ever approve gassing Drones. Storm their lair through main entrance or better send "one man army" to eradicate them, but not gassing.
CAU is not equal to Protectorate ruling elite, they are just very useful and efficient psychopaths.
Drones base is not next to Rail Crossing, it's actually far and under the station, D5 mutagen gas is obviously heavier than air, so there is no danger of contaminating rail tunnel, only Underpassages, already full of all kind of undesireables, so who cares? I found CAU's plan pretty sound. They not just cleaned "roach nest" but also send a signal to all remaining FD around. Mareth loves to incite terror, I imagine a long list of warcrimes they are proud of, and gassing is probably not the most hideous one.