Is it permissible to work for a company that supplies public libraries in Germany with electronic materials—including copies of the Bible—in the field of programming the systems responsible for inputing these materials?

There is no objection to working in electronic systems programming, as long as it is not used for unlawful purposes specifically or exclusively. This is confirmed when the majority of the input materials are permissible, and the presence of books like the Bible in public libraries may be needed by a researcher for purposes of critique, documentation, or other reasons.