How can the verse regarding John (Yahya), peace be upon him: "And peace be upon him the day he was born and the day he dies and the day he is raised alive," be reconciled with what is narrated about his killing at the hands of the Jews and Romans?

There is no definitive text from revelation confirming that Yahya (peace be upon him) died a martyr, and all that has been reported concerning this matter from the narratives of the predecessors is taken from the People of the Book. It has been permitted to narrate from them without affirmation or denial, unless there is evidence. The statement that Yahya (peace be upon him) died a martyr does not contradict Allah's saying: "And peace be upon him the day he was born and the day he dies and the day he is raised alive." For peace here means security and safety from the trials of the grave and the terrors of the Hereafter, and not safety from worldly misfortunes. Yahya (peace be upon him) attained the rank of martyrdom, which saves him from the trials and terrors of the Hereafter, and the martyr is protected from the torment of the grave and is safe from the greatest terror. The safety mentioned in the verse pertains to matters of religion and one's ultimate destiny in the Hereafter, as the word "peace" (سلام) is not prefixed by "al-" (ال) which denotes generality and comprehensiveness, so it does not include safety from all worldly misfortunes. Similarly, at his birth, he was not saved from the sting of Satan as other prophets were, whereas the promised safety for Yahya (peace be upon him) relates to his religion and his Hereafter.