1) Sure, the priest didn't want to lie, but why couldn't he just go to the Catholic church in France for sanctuary instead of go back home to face certain death? Suicide is a sin.
2) If the Guardia's informant, the smuggler, knew where the bandit lived and dealt with him regularly, why not just send someone to his house to shoot him? He was completely unguarded and not living in secrecy (random street kids are able to direct the other kid right to his apartment).
3) Why was the trap at the hospital still set after they had gone to the train station to capture the priest? They captured the priest because they knew he had told the dude about their trap. No reason for them to all be sitting around the hospital waiting for him after that.