Is it permissible for the family of a deceased Muslim to agree to his Christian wife praying over him in the church first, then praying over him in the mosque and burying him in Muslim cemeteries, in order to prevent the harm of burying him in Christian cemeteries?

The Shari'ah came to realize benefits and minimize harms. If two harms conflict, the lesser is tolerated to avert the greater. It would have been better for these people, had they known that the woman would overpower them, to agree with her on holding the funeral in the church, and then they would take charge of it afterward. The harm of holding the funeral in the church is far less than what occurred, namely burying him without washing, shrouding, or praying over him, if their opposition was the reason she refused to enable them to bury him.