philosopher: I said that being physically alive in a kever for 3,000 years is the worst punishment you can give someone… Can you imagine being physically alive in you kever forever?
You’re making the wild assumption that for Yaakov Avinu to be alive in his kever would be ‘unpleasant’. I, on the other hand, assume that if Yaakov Avinu is alive in his kever, he does not find it unpleasant at all. If Hashem wants him to be alive why would Hashem not make it pleasant for him? Yonah, on the other hand, as you wrote, was being punished, so Hashem indeed made it unpleasant for him.