Is it permissible to work on designing a system to automate the procedures of Christian courts (such as marriage, divorce, and changing denominations), and if it is impermissible, is it sufficient to return the money to the company owner, or must the system be restored to its original state before the modifications?

It is not permissible to work on developing a system to automate the procedures of Christian courts, because it is used for and aids in what is unlawful. This includes marriage, divorce, and changes of religious affiliation. Referring for judgment to a abrogated law is an act of disbelief (kufr), and it is not permissible to assist in it, whether the perpetrator is a Christian or a Muslim. It is obligatory to immediately cease this work, return the money, and repent to Allah Almighty.