At the risk of sounding sexist....
If both husband and wife are sincere followers of God and are committed to honoring Him, and if the husband is pursuing God on the matter, they should go to the husband's church, no matter what faults others might see with the denomination.
The husband is the leader of the family and is the spiritual covering over it. He should lead and love and Jesus loved the church, and the wife should be willing to come under that leadership. The wife will be blessed by being in the proper roles of the marriage, regardless of the husband's choice.