Question: I need a mechanism/organism similar to rust and virus, that will both impair the ship's components AND will kill crew, so the only thing left are a few lucky survivors on a crippled ship. Presumably the hull is breached by a tiny comet containing the mechanism.

For the component damage, maybe it just attacks wiring or some electronic components (affect only copper, silicon, semiconductors etc) or certain structural elements (affects only aluminum, carbon-fibre, rubber, etc)

Answer: 
I'll suggest [FOOF](https://en.wikipedia.org/wiki/Dioxygen_difluoride) and then back away very quickly. That stuff is so dangerous I don't even like to *read* about it for fear of getting burned, I don't know if it can occur in nature easily enough that a ship could get hit with it but if it did any survivors would be very lucky indeed. That is to say it does occur in nature but not very often to my knowledge. It is pretty indiscriminate though so if you want to realistically cripple non-contiguous systems with it you'd need multiple tiny point sources rather than one big one.
Humans like to live in an oxidizing environment. Oxygen oxidizes a lot of things and released energy when it does. Humans and other aerobic life forms capitalize on this to get energy.

**You want a life form that can oxidize anything oxidizable.**

We have life forms on earth that can oxidize many things, including iron and just about every component of a living organism. Organisms can oxidize petrochemicals. I cannot think of anything that oxidizes metallic aluminum probably because it does not occur naturally but one could imagine a metabolism like that. Oxidation is a good platform for energy metabolism.

Your organisms are alien microbes that oxidize anything not already maximally oxidized: any metal with an oxide, any carbon except CO2. They are biologically unusual enough that they do not provoke a very robust immune response from humans. They are slow but they are tenacious. In an anaerobic environment they go dormant and wait.

For humans, slow oxidation would be a bad way to go.