Why not the actual death penalty? Or put another way, why not sanctions on the individuals these entities are made up of? It strikes me that qualified immunity for police/government officials and the protections of hiding behind incorporation serve the same purpose - little to no individual accountability when these entities do wrong. Piercing the corporate veil and pursuing a loss of qualified immunity are both difficult - in some cases, often impossible - to accomplish in court, thus incentivizing bad behavior for individuals with those protections.
Maybe a reform of those ideas or protocols would be useful and address the tension you highlight between how we treat "individuals" vs individuals acting in the name of particular entities.
As an aside, both protections have interesting nuances and commonalities. I believe they also highlight another tension (on the flip-side of punishment) between the ability of regular people to hold individuals at these entities accountable in civil suits vs the government maintaining a monopoly on going after individuals. This monopoly can easily lead to corruption (obvious in the qualified immunity case, less obvious but still blatant in the corporate case, where these entities and their officers give politicians and prosecutors millions and millions of dollars).
As George Carlin said, it's a big club. And you ain't in it.