What if you were Christian and now you are atheist?  You will be warned against the genetic fallacy. That is the idea that if you are Christian and leave the faith that does not mean you have to abandon all the values that Christianity gave you. The spurious origin of a principle does not make it wrong or mean that you have to give it up when you are no longer believing the system that gave it to you.  1 and 1 remain 2 regardless of whether the school is an atheist one or a Christian one.

If I am Christian and don’t steal and pay all my taxes and don’t cheat on my spouse and become atheist I may continue to do these good things.

I don’t have to abandon the values I live but I do have to abandon them as specifically Christian values. If I am faithful because God banned adultery, now I am faithful not because of God but solely because of my respect for my spouse.