One is expected to avoid working for an employer whose primary line of activity is impermissible. This is different from working for oneself or a company and then, as part of one's work, providing services to such an employer.
Thus, it would not appear to be permitted to be the employee of a Church, even if one's own work itself is permitted and not a direct assistance in the impermissible activities (such as non-Islamic religious activities). We respect other religions and their right to worship and practice as they see fit. We let them be, respect them, but don't actively assist them personally in their worship-related activities--though we should haste to defend their recognized rights if these are being attacked, and also cooperate with them in the promotion of good in society and for common causes.