Separation of church and state is part of the constitution, not up to school discretion.
Did any of this actually happen on a national scale? Are you talking about forced prayer and not all prayer? I can see a district dealing with these things, but I don't think it's national policy yet.
In my high school we say the pledge every day, and nobody polices the halls saying I'm not allowed to pray.
This is an entirely separate situation than dealing with condoms. The reasoning behind getting rid of forced prayer and forcing kids to say "under god" in the pledge, is that there is a law requiring the separation between church and state. The law will always come before personal preference in schools.
If it was deemed illegal for anybody under 18 to touch a condom, then it would only take one parent to get them removed from school grounds, but that isn't the case. Condoms are just a safety tool, and it will take way more than just one teens parents to change school policy.
edit: More info on the pledge of allegiance.
In 2002, Elk Grove Unified School District v. Newdow, he challenged the pledge of allegiance being taught to his daughter in public school. It was thrown out of the supreme court because he wasn't the custodial parent.
In 2006, Frazier v. Alexandre, a 1942 law requiring that students to stand and recite the pledge of allegiance was deemed unconstitutional based on the first and fourteenth amendments.
Document of the Frazier v. Alexandre case