In many cases (e.g., no warning, no witnesses) a capital crime is not punished by a beis din, but instead the offender gets kares. Let's assume for the purposes of this question that kares includes punishment in the afterlife (and is not only dying before one's time).
Now, from this answer it almost seems that punishment by the court is better than an afterlife punishment. There we have an offender whose crime is so heinous that he can't get a kapparah through beis din's execution. Presumably, though, he still gets punished in the afterlife. So we see that punishment in the afterlife is a greater punishment, and that that offender wasn't 'deserving' to get the lesser punishment on Earth. Thus here we have kares > capital punishment
But how can this be, if kares is usually given for less severe violations of the same sin? If someone is warned by two witnesses and still blatantly continues doing the sin, that sure seems like a more severe offense than if he did it in private, overcome by his passions. So we really ought to have capital punishment > kares.