The pirates were pretty panicked. Logically speaking, it probably would have made more sense for the two survivors to run, or attack the Monks. But people don't think logically when crazy kung fu bitches start beating you to death, and then a sea monster comes Up From The Depths.
So they attacked the sea monster. I mean, why not? Why not Zoidberg?
Their swords bounced harmlessly off of Zoi-Akaiji's armored carapace.