Sure, it is permissible. Churches are for God worship as Mosques. However, the Muslim engineer should not participate in making the structural engineering of what is against Islam religion, as a statue for Jesus or Mary, structures for ritual worship that is related to Jesus as God or son of God, ... etc.
Thanks for your answer. May Allah reward you for that. but in churches they worship Musa (A.S.) (Jusus) not the God. Therefore the cause of it is wrong. Any help is appreciated.