All perfect praise be to Allaah, The Lord of the Worlds. I testify that there is none worthy of worship except Allaah, and that Muhammad is His slave and Messenger.
Opening the school day with the recitation of the Quran or with any mention of Allaah is a good thing, and this proves that you are keen on doing good; may Allaah guide you even more, and increase your piety and righteousness.
However, you should not always recite a specific Surah (chapter of the Quran) or a specific mention of Allaah, as this may falsely indicate that this specification is an act of Sunnah and this may render it an additional innovation. For more benefit, refer to Fatwa 89796.
Therefore, you did well by stopping the regular recitation of a specific Chapter. It is more appropriate to set a programme in the morning assembly that includes various activities, like the recitation of a Chapter of the Quran, recitation of a Hadeeth, a mention of Allaah, a proverb, or general knowledge, as this will benefit the students much.