I strongly believe that a lot of a chinchilla's personality is genetics. I have had 3 chinchillas from ranches. Out of those three, Marlow (RIP), who came from a ranch with more than 1,000 chinchillas, was the sweetest chin there could be. He was sweet from the moment I brought him home. He couldn't have possibly been handled much, if at all, in a ranch with that many chinchillas. I got my chinchilla Charlie from a ranch with only 150 or so chins. He is a little monster. Sure, he's improved from the first few months when he cowered in the corner and only wanted to go after me, but he's still skittish and doesn't really enjoy any sort of affection/attention. Sure, it could be because he wasn't handled from the ranch he came from, but then, how do you explain Marlow that came from a ranch 10x it's size? And Spader came from the same ranch as Charlie, and while he's not aggressive, he still doesn't like to be messed with a whole lot. I finally got to the point where I can pet behind his ears, but he'll go from enjoying it to arching up at me in a matter of seconds. Now, I do realize none of these behaviors are necessarily aggressive and I never claimed they were biters. I simply brought up these cases to show the difference in temperments in chins that were never handled from day 1.
When I do finally move out and get into breeding myself, if I ever had a pair that produced aggressive kits, then yes, I personally would seperate them. Then again, I do strongly believe that a chinchillas' temperment has a whole lot to do with genetics.