The reason why the extinguisher received its immunity during cooldown was purely from a design standpoint. The reason is as follows:
The extinguisher is meant to be a reactionary tool. You see fire, you go over to extinguish it no matter how many charges there are. If you don't respond, you are penalized by the DPS that fire does. The problem was that if you respond successfully, during its cooldown (where you can't respond any more) you can accumulate more stacks. Not being able to respond in this situation denies the player of their intended play style.
While there weren't many complaints regarding this, it's very poor design. I'm confident enough to say that you also felt this wrong on a subconscious level but just dealt with a crap design.
Now, the ramifications of immunity during cooldown means that the component will be taking less DPS. However, the situation is still similar in that if a component catches fire while cooling down (old extinguish) or an enemy is still flaming you and ignites a component after cooldown (current extinguisher) you are still required to respond. Difference is that the system doesn't render you helpless (can't extinguish during cooldown). You always had the ability to sit at a component and baby it with the extinguisher.
What comes out of this, again, is less damage on the component overall. Because we don't deny your ability to extinguish now, you can theoretically respond perfectly to all fires on the ship and take no damage at all (impossible, of course). Before, if you respond perfectly you'd still fail because stuff would still be on fire during cooldown.
While this is better than the gunner thread, please go into matches with flamers and take a closer look at what is going on.
It may be true that chem spray, the preventative tool, may be very difficult to pull off. Again, it might be something that a higher level engineer would do. Idea is that chem spray engineer never stops running around. Probably, buff/chem engineer.
Now the question is, what changes can be made to make prevention feel more like prevention? I think extinguisher is right now.