I been pondering this over, I think part of the problem is that fire and chem spray both share the same cooldown together with repairs. Which I while reading this thread seem to be a common theme to everyone suggestion. It's hard to pick chem spray over fire ext because you have to pick which of the two you use.
Remove shared cooldown and lower immunity to 1 seconds (fire ext can't be used again on that part for 1-3 seconds), removes a high amount of stacks but not all stacks. Chem spray can still be used at the same time. It should be balanced so that if you hit full stacks on a part, you can't remove all stacks with chem spray + fire ext but at least you can reduce the stacks to a management level that next fire ext cycle and possible chem spray cycle, you can remove it all. This means you could have a "firefighter engineer" build now. At the cost of being able to repair they could deal with fire easily enough.
I actually have to go now, I'll come back to either post more details or edit this post depending. BRB