As much as this is a neat idea, I don't think it'd be Responsible to go mess around with core combat mechanics at this juncture
Plus, the AI work this would require, *shudder*.
It's an interesting theoretical question, though - would this sort of thing be good? I can see it working in Doom, but isn't the end result that you're not really at your weakest when you think you are?
With the caveat that I'm entirely unfamiliar with the specifics in Doom: it's more of a gameplay flow thing there, right? It's not that the design wants you to be weak at a certain points, but more that it wants you to do something else (which is cool to boot) when the normal approach runs out of steam. It's there for variety, possibly to keep gameplay fast, and probably to make sure that progression doesn't stall out when you run out of juice (i.e. you're not in a weak state, just a different one).
In Starsector, venting needs to be a vulnerable state. Quick example: missiles! If this "venting damage" could take out missiles (and it'd be kind of weird if it didn't), then that would pretty much break missiles straight up.