1) it’s rare, if ever, that a CEO, CFO or COO faces jail time for crimes the company committed that are similar or worse compared to jail-able offenses by individuals. So your second point doesn’t really happen in practice.
2) shareholders SHOULD be punished for the actions of the company. If my dog maims you because of my negligence to control it, I’m liable. If a corporation knowingly commits crimes, then the CEO (and everyone in the chain down to whoever performed the criminal action) is a criminal, and the board and the shareholders should be liable for not exercising proper control and guidance. When you own something you also take on responsibility for that object. Stocks are no different.