While I see where you're coming from, it still has its issues. Let's take Voices of the Void for example: you spend most of the game afraid of the aliens, because at any moment, they could show up, and you know you can't outrun them, or hide from them if they spot you. However, by the time you realize they're harmless, it becomes less scary and more annoying to be interrupted by it. My point is, suspense and the feeling of helplessness against a superior enemy goes away.
Now copy paste this to most other entities in the game. The only threatening things in VotV are certain wisps, and the physics based damage system. Shadow people popping up is spooky the first time but loses its bite once you realize they too are harmless. Same with Anti-breather. I'd actually agree that adding something to defend yourself with would ruin things but with the caveat that the horror itself is already dull.
Also, the Alien builds up a tolerance to molotovs and the flamethrower if you use them too much, and will start testing the limits of it more and more as you do so, so not even the flamethrower keeps you safe for very long.