There isn’t one easy or simple answer to your question. I believe the first step is always to pray. First we pray, then we act. First we pray, then we talk. First we pray, then we speak up. If Christ is indeed the Lord of the church, then he knows the truth about the church, every part of it, much better than you do. So we pray first.
Then comes the negative. Beware of gossiping and complaining, even if you know you are in the right. Gossip is a terrible sin that divides churches. Just because your observations are true doesn’t mean they need to be broadcast to the whole congregation. I don’t mean you shouldn’t make your concerns known, only that it should be done in the right way.
Go to the pastor.
Go to the elders.
Write to the leaders.
Express your concerns.
But do not demand in advance that they act in accordance with your wishes. Your job is to express your concerns thoughtfully, graciously, firmly, biblically, and then leave the matter with the Lord. Perhaps others unknown to you also share your concerns. Your speaking up in the right way may be used by the Lord to promote change.
What if nothing changes and you come to have little confidence in the leaders of the church? In that case, you must leave the church. Leave quickly, quietly, graciously. Don’t make a big deal about it. Don’t feel like you need to help others “understand” why you left. Just leave and find a church where you can worship with a clear conscience.
If leaving is not an option (for family reasons or because there are no other church options or simply because you choose to stay), then your final resort can be put in three words:
Stay and pray.
Stay and pray that God will change your heart. Pray that you can come to love Christ’s church just as it is, warts and all. Pray to be delivered from a judgmental spirit. Pray for new love for all the saints. And take a vow of silence that having done all, you will not speak of your concerns again. You must guard your own heart lest Satan use your discouragement to get a foothold in your life (Ephesians 4:26-27).
Churches tend to change slowly. You normally shouldn’t expect a quick sea change in your congregation. But give God time to work in every heart, including your own. Over time the leaders may change, the atmosphere may change, the Lord may do a great work. And while you pray, keep your heart open, remembering this ancient prayer: “O Lord, change the world. Begin, I pray thee, with me.”
For further thoughts, see my article How to Leave a Church.