Following the hundred days and the defeat at Waterloo, Napoleon decided to give himself in to Captain Maitland. In an age were international law was still coming into existence, honour was still the primary guide for 'proper' behaviour in these situations, let's not forget the British were also duty bound not to kill a prisoner who had openly surrendered to them, even more so when he had been a head of state. It is possible, that had Napoleon turned instead towards his own country, that he would have indeed faced trial and eventual execution, to prevent him from trying to rally more troops for yet another war.

Moreover as strange as it may seem, Napoleon was also very popular with his enemies, particularly the British. Many people in Britain viewed Napoleon as a military genius, a romantic figure, and the mythology of his life was already well under way even before his death. Even Parliament wanted him treated better.

Another factor I would say is that Napoleon always had his supporters in France, although this became less so as he sent an increasing number of French soldiers to their deaths in battle. He had given them a few very honourable years. This meant that by killing Napoleon the French would be running the risk of spawning an angry revolt and further continuation of hostilities in an already hostile time.This is probably a very dominant factor that accounts for why he wasn't executed following his first capture or neither upon his return from exile.