We have consistently had religious education classes in many European countries and they do nothing. Most students are bored to death, and most teachers do not take it seriously.
The fact that the bible is shoved in education is a bad thing, yeah, and it does showcase how messed up the world is.
But I wouldn't worry in the slightest that this "affects things negatively". It's water under the bridge, christianity is dying and nothing can revive it.