There are definitely some steps you can take to avoid damage via contaminants, I wouldn't say they're an immediate "you lose!" but you do have to take some extra precautions. It does change the feel of the game a lot though, the game suddenly turns into some bio-warfare horror story
. I think it's pretty awesome but it should probably be more rare than on every other FB, which probably arrive too often anyway.
One thing I've noticed is that washed-off contaminants on the ground are safe to clean, so as long as no one is covered by them and the contaminants aren't in a direct path dwarves are using, you have some hope of cleaning up the mess without serious issues. It's hard to get dwarves to clean though, I wish there was a designation.
Take a second look at the FB's status page before deciding how to kill it. If it has
any form of syndrome, expect any dwarves going toe-to-toe with it to die. So far most syndromes I've seen are pretty lethal, or at least leave permanent scars. No matter how you kill it, if there's a corpse left, forbid the corpse immediately. You can lock it off (or even wall it off) so no one accidentally walks through.
If you have dwarves that are contaminated, you can temporarily wall them and create a decontamination booth. Have dwarves dump water into the booth from above. 1/7 depth is enough. From the couple times I've done this, I'm pretty confident that even while water is still in the booth you can then let the dwarves out and what you'll end up with is only contaminants on the ground, but none covering your dwarves. These can then be cleaned safely. Unfortunately the exposed dwarves will get ravaged by whatever the syndrome was, and might still die. But as has been pointed out, none of the syndromes are contagious.