While I can think of some hand gestures (eg flipping off the other teams) that could be considered as poor sportsmanship, I don't see how you can go so far as to interpret something like pointing to heaven (or even crossing oneself) as excessive celebration.
I also don't see a "separation of church and state" issue here, as long as the school is not requiring or encouraging kids to engage in a particular ritual.
These are kids, for crying out loud. If they did something remarkable, like getting a new personal best, they should be allowed to celebrate within the bounds of good sportsmanship. As long as they aren't taunting the other teams or engaging in a prolonged celebration that is keeping them from shaking the other teams' hands in a timely way, I just don't see what the big deal is.