Convent or Christian schools are private schools so what's wrong with Christian prayers? I went to a Convent school as a kid. We learnt about Jesus, Mother Mary, and did Christian prayers; so what? Am I Christian today? Same thing in the West, there are plenty of private Catholic schools and there is nothing wrong if they do Christian prayers in the morning. Infact in the West, if you are a Catholic, the school will give you a big discount and your kids will have to pay less fees, but if you are a non-Christian who wants to attend, the fees is actually higher! So some folks actually convert to give their kids a better private education. A lot of Chinese do this, and I know an Indian family who has also done this.
That being said, these are all private schools, but the school in question is a public, government-funded school! So you can't make a comparison there!