This is The Eichmann Variations by George Zebrowski (h/t to @DCoder for the suggestion).
After capturing Adolf
Eichmann, the Nazi hunters clone the criminal and execute the replicas
-- recognizing the barbarity of eye-for-an-eye, but seeing no other recourse but to equal the loss of Jewish life with the repeated taking
of Eichmann's life. The morality of creating innocent beings to be
sacrificed to the grist mill of Eichmann's projected guilt and the
victims' principles for existence is combed over with a surgeon's
precision and a satirist's wit.
It certainly seems to fit the description, has been repeatedly anthologised since its original publishing date and is less about the actual story and more about the philosophical and moral dimension.
A world benefiting so greatly from Israeli science and technology looked the other way when I was kidnapped. Nazis were merely a strange
and rare form of humanity collected by their Jewish benefactors, for
“It is the best we can do, anyone can do. Six million German flesh
for six million Jewish. German flesh created by our conscience, from
our soil and the sunlight of God, Mr. Eichmann.” I stared at him and
answered, “Innocence in your eyes is not the prize you think. I
“Shall we stop then?” “No—that would waste all that has gone before.
He will live and he will die. Maybe we’ll learn something yet.” “But
how can you even hope?” “If even one variation repents, I’ll destroy
the original and close down the project.”