I think you're missing the point. The issue here is that we have two prosecution regimes at work: one for the banks which works by more or less the rules you propose, and one for "everyone else", which very much doesn't. Your idea of only prosecuting bank employees with direct connection to the crimes seems like cold comfort to all the people threatened with arrest, in prison (or hell, even shot) because of the activities of their husbands and roommates.

Strangely, libertarian hacker types tend not to come to their defense as quickly as they do bank executives.

Of course the outrage comes from the fact that corporate structures offer so many layers of plausible deniability. At the end of the day, we would have to be fools to believe that billions in money laundering or price fixing are happening at these banks orchestrated, as the executives would have us believe, by a small group of malevolent peons expertly covering their tracks. It's just common sense that lots of people know what's going on and turn a blind eye because it's good for business and there's virtually no chance it'll actually get pinned on them.

You can go to prison for being an accessory if it can be shown that you were consciously aware that the crime was going on but did not stop/report it, or that you not being consciously aware is due to gross negligence on your part.

In the US, something like this is already a crime under Sarbanes-Oxley.