Pete figures out that the Prince is in the village, so he plans to make sure the Prince doesn't get back to the castle alive. That's all well and good. But then, when Pete and his henchmen find the Prince, they take him back to the castle... alive! They do lock him in the dungeon and plan to execute him later, but still, why leave him alive in the first place? You could argue that Pete needed to be back in time for the Pauper's coronation (if Pete wasn't there to threaten Mickey, Mickey probably wouldn't have gone through with it.) But why not swoop in, kill the Prince in the village, dump his body somewhere on the way back to the castle, and be done with it? If they were able to capture the Prince in time, would it really take that much longer to kill him? You had a solid plan, Pete! Why contradict it?
Out-of-universe, there are two obvious reasons: One, Bond Villain Stupidity is a common trope because it gives the heroes a chance to win. Two, this is a family-friendly cartoon, and they wouldn't allow such violence. But is there an in-universe reason?
