The practice of only fining a business for clearly illegal activities creates a dangerous precedent that the rule of law is optional, and when broken can be boiled down to a "cost of doing business". This creates an environment where the people who run these companies have zero liability for the illegal activity of their company, if only they are able to succeed long enough to be considered "too big to indict".
The logic that a company is so large that their being penalized in a criminal fashion would destabilize the economy should be a trigger that the company is TOO BIG! While the government takes a "hands off" approach to such large companies, the investments (namely IRAs, 401ks, etc) of hardworking Americans are put at greater risk.
We're at risk BECAUSE they are "TOO BIG".