Your Question: Should I obey my Pastor
The short answer to this question is yes, though the Bible does expand things a bit more.
Pastors and elders have been given the responsibility to lead and care for the flock (Christians and church members) and as such we should obey them (Romans 13:1-2, Hebrews 13:17), just as Moses was God’s representative before the people of Israel. If they sin or do something wrong they will be punished more severely than people who are not leaders (James 3:1).
However there are times when a Pastor or elders maybe begin to use their position for their own ends. Sometimes they may try to force people to obey them, saying that “God says”, or “the Bible says”, but actually they are trying to manipulate people to do as they want them to, which has nothing to do with God. This is why it is very important that every church member reads, knows and understands what the Bible actually says. But accusing or complaining about a leader that God has established is a serious thing.
1 Timothy 5:19 states that an accusation against a leader must have more than one witness. If we find ourselves in a position that we feel our pastor is wrong, there are a few steps that we need to follow, in order to resolve the issue. Matthew 18:15 – 20 addresses this issue:
1) make sure you have all the facts right;
2) first go to the Pastor, elder or leader that you feel is in the wrong, and tell them why you are unhappy with them, or what is being preached or what is being said;
3) if the pastor/leader, is not able to explain how or why things have been said or done go to another leader of the church. Explain the situation and why you feel it is wrong;
4) if the other leader or leaders feel that you are right in your challenge, then you, plus the other leaders of the church need to go and talk with the pastor;
5) if the Pastor still does not repent or accept that he is at fault, the leaders need to take steps to discipline or resolve the situation.
As for you, you should pray for the Pastor, and in the event that nothing changes, leaving your church maybe something you should consider.