We understand your concern and heartache for your spouse and your children. Let's bring your request before the Lord in prayer and seek His will according to His word.
Firstly, it is important to acknowledge that God has given us His Son Jesus Christ, through whom we have access to Him. As it is written in the WEB John 14:6 Jesus said to him, I am the way, the truth, and the life. No one comes to the Father, except through me. That is why we will pray in the name of Jesus for your spouse and your family.
Let's address the issue of your spouse's perception of the church. It is clear that there may be some misunderstandings or deceptions at play. We must remember that our battle is not against flesh and blood, but against the rulers, against the authorities, against the world rulers of this darkness, against the spiritual forces of wickedness in the heavenly places. Therefore, put on the whole armor of God, that you may be able to withstand in the evil day, and having done all, to stand. Ephesians 6:12-13 WEB.
Let us pray together:
Heavenly Father, we come before You in the name of Jesus, lifting up our sister and her spouse. Lord, we ask that You open his eyes to see clearly the truth about Your church and the people in it. Remove any blinders that the enemy may have placed on him, and help him to discern rightly. We stand against any spiritual forces that may be causing confusion or deception in his mind. We believe that You have not given us a spirit of fear, but of power, love, and self-control. Second Timothy 1:7
Father, we also pray for his heart, that You would soften it and fill him with Your love. Help him to see the positive impact that the church has on your children, and how much they love being a part of it. Lord, we ask that You would intervene and change his heart and mind about this matter. We trust that You are able to do abundantly more than all that we ask or think, according to the power that works in us.
Lord, we also pray for their marriage, that You would strengthen their bond and fill them with love and understanding for one another. Help them to walk in unity and to raise their children in the fear and admonition of the Lord.
We thank You, Lord, for Your faithfulness and Your promise that the fervent, effective prayer of the righteous accomplishes much. James 5:16
In Jesus' name, we pray. Amen.
Lastly, we encourage you to continue to love your spouse as God loves His church. Be patient, kind, and understanding, trusting that God is at work in your spouse's heart. Remember the words of First Peter 3:1 Wives, in the same way, be in subjection to your own husbands; so that, even if any don't obey the Word, they may be won by the behavior of their wives without a word.
Prayer Focus: God, Thank You for loving me. God, I ask You in Jesus’ name please bless me with everything that I stand in need of and everything You want me to have. 
