In Yoma 86a we find the following Tannaic statement
If one commits a transgression that warrants karet or a sin punishable by death from the earthly court and then repents, repentance and Yom Kippur suspend his punishment, and suffering absolves and completes the atonement
So if someone is found guilty of a capital offense by a beis din, but prior to that he has already repented and a [at least one] Yom Kippur has passed.
Wouldn't the above statement imply his punishment should be suspended - and he should not be executed? (And if you say "but suffering completes the atonement", suffering is not the same as actual death/execution).