My understanding is although Halogen kills ozone it is so good on all types of fires that Aviation has a dispensation to use it.
If you were going to use any form of extinguisher in a cockpit wouldn't it be because of fire and wouldn't you have smoke in the cockpit and therefore would you not have to vent the area by say opening a door.
Seems to me getting sick from halogen may be less likely than burning, and lets face it how many times has the average chopper had a fire in the cabin