You are mistaken, it just takes a while for the room to vent properly and them to start taking damage (when there is a yellow outline around the room people start to suffocation).
Are any of the dudes immune to suffocation cause that seems like a reliable way to suppress fire and intruders all at once.
The bots are immune to suffocation (personnel drone, boarding drone, repair drone), but they are pretty useless overall (compared to regular crew members at least, or attack/defense drone).
Fire in medbay-> Vent out medbay-> Wait till fires go out-> Press "close all doors" button (to close the doors to space)-> Press "Open all doors button" (which won't open the doors to space).
You don't really need to open the doors, but it does help it equalize a little faster (which won't really matter, but it might help by a second or two).
Obviosuly that doesn't work if there are a bunch of enemies on board, but as long as you have doors upgraded you should be able to get them with strategic venting (eg. having the door they are trying to break into already vented, so when they break in they have no oxygen there).
The two best anti boarding ships IMHO are the A) Zoltan ship (its super sheild allows you to stop boarders until its down and have all the non-crewed rooms vented if you see a teleporter on their ship, break through your sheild and tele on you can just trap them in the vented rooms), plus it starts with Doors 2 B) Engi ship, its global heal is super useful for fighting boarders and surviving oxygen problems.