You don't need the equivalent of capital punishment for stealing and, by extension, don't need to take away all of a caught thief's money, just a sufficient multiple of their stealing to make it unattractive to enter into a career of it.
So the point is not simply that you need to defer thieves from entering a career of it, but that you need also to deter thieves from considering it as a one-time option for when their quarterly earnings are due, and that you need to do so sufficiently well that even a highly skilled thief with a multi-million dollar company salary won't consider it. So either it can't just be fines (asset seizure/prison, maybe for repeat offenders) or those fines must be legitimately severe as measured by the one committing the act.
you might reasonably assume that if you catch a company engaging in one instance of illegal activity, you have only seen the tip of the iceberg and there is much more that you couldn't prove. I would prefer the government not to be setup on this premise, but as I said, this is a philosophical position.
The large bank can continue to do damage if they are caught, while the small one cannot. Thus they definitely do more harm, and at the very least will be perceived to have effective immunity from the law.
If you only fine thieves proportional to the value of the stolen goods, then all you're doing is saying it's ok to steal so long as you are sufficiently wealthy. (And if you became wealthy through theft... then you've made a legitimate living through damage to society.)