Rust doesn't give you tetanus, so you can relax about that
(You may be thinking about the stereotypical 'getting tetanus from stepping on a rusty nail' scenario, but the rustiness of the nail or lack thereof has nothing whatsoever to do with getting tetanus -- tetanus is caused by a bacterium that grows in conditions that lack oxygen, such as the puncture wound you get from stepping on a nail)
I would seriously doubt that the rust (which is just iron oxide) itself would hurt chicks, although that is a guess/assumption rather than Documented Fact. However, I'd worry that there might be rusty *rough* spots that could damage their feet if they scratched down thru the bedding in the wrong place.
If it were me, I would not get rid of the trough, but I would sand it down (wear a dust mask, rust dust isn't great for your lungs) then paint it with a couple of coats of either rustoleum or epoxy paint. The epoxy paint is more expensive, and you NEED TO wear a fume type respirator mask, but it will last a lot longer than the rustoleum in damp conditions. OTOH if you only ever use the trough for brooding, and store it in a dry place between batches, rustoleum is probably sufficient.
Good luck,
Pat, who spent many a day in grad school painting the insides of metal stock tanks with epoxy paint for her dissertation research
