Any way to make your crew stop attacking a system

There is an augmentation "Weapon Pre-Igniter" that powers your weapons instantly when you come out of the jump. But even with this it is very hard to stop the teleporter. You need to either have sufficient firepower to bring down the shield and teleport station in one go. Or have enough shield bypassing or enough EMP firepower to be able to bring down the teleport station.

You also need to keep it down the whole battle, if it is repaired for a short time it will probably instantly teleport boarders on board. (This I think, I have not tested this).

When I had a ship with the Weapon Pre-Igniter, I never was able to stop the teleporter quick enough to prevent boarding from taking place. I have not tested this very extensively btw.

Taking out the teleport pad does prevent them from returning to their own ship, a blessing and a curse. (They do not teleport away before you can get the EXP. But on the other hand, you still have boarders on your ship)

The enemy can't teleport to a cloaked ship or retreat their troops from a cloaked ship. So you can use Stealth Weapons augmentation and cloaking to blast away the teleport pads of the enemy ship.

And, the Zoltan Shield also prevents ships from teleporting boarders on board. (Events still work).

When the door subsystem is damaged, you cannot open the doors yourself. Crewmembers can open them by walking through them, although I doubt this is useful in a situation where you're trying to vent a room that is on fire.

Eventually, a fire will burn out the oxygen in a room and put itself out, although depending on the strength of your doors, this may be after it's lit nearby rooms on fire.

Personally, any time where I think I'm going to be in a situation where fire is an issue (ie, the "too near a sun" events) I'll preemptively vent as much of the ship as possible. That way, if a fire does break out, it's more likely to burn out quickly.