Without reading the bank account agreement and seeing the bank charges, I can’t say if the $268 they are seeking is right. It’s not clear how the bank arrived at the extra $100 just from what you wrote.
Taking the money to the bank will only fix the civil problem and thus prevent him from being sued for the money. What he did almost certainly qualifies as fraud, an repaying it does not make the crime go away. If may affect whether the prosecutor decides to pursue it, and could also affect how serious any sentence would be if he were convicted.
Your step-son should probably see a criminal defense attorney for advice. Hopefully he understands now how stupid it was to do what he did.