A particular implementation of Intelligent design has been adjudicated to be non-science in a ruling that applies to one school system in a particular federal district. The ruling is not binding on other parties even in the same district.
You are correct.
That said, there is little the executive branch can do about that, and at least one part of the legislative branch seems more likely to pass an 'Academic Freedom' bill suppotting ID than to pass anything endorsing the separartion of Church and State.
That is part of the point. The petition is worthless. The things it seeks to outlaw are already largely outlawed. The problem isn't that there are laws allowing the teaching of Creationism and ID in schools. The problem is that the curricula of schools is determined largely by local panels of non-specialists (parents, business owners, clergy...). If they choose to include Creationism or ID in their school's curriculum, then it gets included. If no one complains about it being there, then it stays. The current way we build curricula is faulty; plain and simple.
It might feel good to tell the federal government that it can't teach Creationism and ID, but it is of little use when the federal government has such small say in what shows up in the classroom to begin with.
In short, this petition barks up the wrong tree.
Love your enemies!