Why does One Piece antagonist disappear after being defeated? Let me take an instance of one villain: Arlong. Arlong got defeated by Luffy, he wasn't killed. Luffy didn't stay in Kokoyashi village either. So Arlong could have returned to his usual business of enslaving the village. He would have faced ugly humiliating words from Villagers initially, but why would it matter? All you gotta do is gang-up on them. No one in the village was strong enough to stop them. 

There are many other pirates who just disappeared after being defeated. It's not like they lived their life with principle or something, they were bad guys who used to loot, cheat, and kill people. Why wouldn't they continue that after being defeated?
In most of the cases, the big villains we've seen have been arrested by the Marines after they were defeated, so they would not get such an opportunity. We see most of them in the Impel Down arc, locked up.

Specifically, in the case of Arlong that you mentioned:


   It is currently unknown where Arlong is being held, since we didn't see him 
 in Impel Down, but he is being held by the Marines somewhere.