Is it really a victory if the case is settled out of court?
It's at best a draw - nothing is resolved.
I'd say yes, because the school district has agreed that they violated the First Amendment rights of the church. If they'd made a financial settlement without a clear agreement on the principle, then that wouldn't be a victory that made the free speech point.
When I looked again at the article, they said, " ... both sides now agree on the legal principles that regulate equal access to school property for community groups." I'm not sure whether, in practice, that means the church puts their sign up, or whether "equal access" means there won't be any community signs!