Is it forbidden to continue working in this institution, given that the questioner is compelled to do so and is forced to be present in the church with Christian students?

This work involves two prohibitions: First, working in the service of a disbeliever (kafir), which is forbidden because it entails humiliating a Muslim. Second, attending his prayers and rituals that involve disbelief (kufr), which is a great evil that must be denounced. If one is unable to denounce it, then he must leave the place. Therefore, it is impermissible to work in the service of a Christian and go with him to the church. Instead, one should request to accompany Muslim students with special needs.