He really did struggle with this, re: the origin of the Orcs, whether they had souls, whether it was ok to default to massacring them without second thought, etc. He never really resolved it.
Most Tolkien fan communities are aware of this dilemma, it's one of those well-known things, along with "did Balrogs have wings?", "couldn't they just fly to Mount Doom and drop the ring?" and "why did Sauron need to put his power within a ring, anyway?".