We don't struggle with flesh and blood, but with the powers, principalities, and those dark spiritual forces of this world!
And to achieve victory in our lives we must walk with Jesus Christ, while in that struggle.
So, what does that mean concerning the concern expressed in the OP?
Well, first of all I am not following a "Church", but I am part of His church (body) if I am following Him (Jesus Christ) - and He leads us out with His voice.
So the church, and Christian building and the people there, are not telling me what to do. He is! Because the church which He has me attend (the buildings and the people there) is a Christian church, they in general are also people hearing from Him at times. Like me, they obviously don't hear from Him as much as they should, so I encourage them and myself to listen to Him more. However I don't struggle with them, because I don't follw them - I work with them!!!
It is important to understand that He is the head of the church, and so He has me working with others who also are in His body!! So He tells me to work in a ministry, or He doesn't. If He tells me to work in a ministry, of course there is going to be levels of authority that He has put in place, but that just means that I don't struggle with them, I work with them as someone under authority! If I feel like there is a problem, I don't start leaning on my own understanding of how to handle it, do I? Ok, sometimes I do, but when I again get smart I remember to take all thoughts captive to Him. Does He still want me in that ministry? Does He have something for me to do concerning that problem? Is it not really a problem at all, but just something that comes up to get to where we need to get to? These are questions for Jesus Christ, and His sheep are supposed to be hearing His voice!!
So do we? Do we take our thoughts captive to Him?? Are we really making Him our Lord?? We are not just leaning on our own understanding, are we?
The point is that we need to be asking Him questions concerning our lives, and be doing that every single day called today!!! And even encouraging others to do the same!!
So in answer to the OP - if anyone is having a problem at there church and feel that the church is not leading them in the right direction - they need to stop following the church and return to following their Lord Jesus Christ, via His voice, so they are part of His church!! The church doesn't tell me what to do, He does, but since it is His church I am working with them as part of Him who tells me what He wants me doing!!
THIS IS A VERY IMPORTANT ISSUE!!
He had me working in a Christian healing ministry for five years. During that time I came across many discouraged and upset Christians who were trying to follow instructions from the church, thereby making the church their Lord instead of Jesus Christ!! So Jesus Christ was not their Lord, some church me member was, and that causes problems!! When they came to the healing ministry, the very first thing we had to do is turn them back to Jesus Christ and get them to start listening to Him!! We all have a responsibility to listen to Him! Not doing that is going to be a problem, and is that not the real problem we see in the OP?
I'm going long, but let me give a specific example (one of many). There was a pastor give a class at the large Christian church He has me attend. The class was about the gifts we have. They did a test in the class showing what skills we have. The thinking was that the test showed our spiritual gifts, which seem dubious because it seems to show our physical gifts. That pastor (not the senior pastor) explained that he used the test results to determine who to hire to help him at the church. So I asked that pastor if it would not be wiser to talk to the Lord about who to hire, and he blew me and my question off, obviously not agreeing with the concept. But that didn't give me a problem, because I was going to do what myLord tells me, even if he wasn't.
Now a year or two later I was serving in a ministry where at the end of another class used for healing, they would have us minister to those in that class. A young man walked in who I had not seem before, but the person ministering with me a leading told me he wanted to stay out of this situation. He apparently knew about something which I didn't. However I started to find out really quickly what the problem was, because the Lord started talking to me about it. The Lord started telling me that He knew about the problem and that He loved that man. The Lord started explaining that He (our Lord Jesus Christ) was not behind the problem! As I was hearing from the Lord I was passing the information on to the man. It turned out that the pastor I had given that class a couple of years earlier had hired this man to work under him. That pastor had convinced that Christian man, who wanted to serve the Lord, that he should work under him, yet that man had hoped to become an engineer. In fact that man knew He had a calling from God to become an engineer!! He knew it. He had heard the Lord tell Him that! But that pastor leaning on his own understanding based on the gifts test, had wanted this sharp young man to be his assistant, and so got him away from His actual calling from God!!
That poor man - he had not entered engineering school because of this. He and his young wife were living in a room at his parents house and were very unhappy, when he might have been close to graduating from engineering school with the hope that he, his wife, and their spirits needed. So the problem was there in the church, and even the man ministering with me knew about the problem because he knew this man. And let me tell you, the Lord our God new about the problem also. The problem is that His people don't listen to Him like they should!!!
So, the pastor was unintentionally leading be into problems, the man was leading his wife the wrong way, there was a problem in the Lord's church which apparently was becoming a well-known problem to those closely connected to the office at the church. And the Lord had been trying to being light on the situation for a couple of years, but His people were blowing Him off instead of seeking Him and His voice!! So lives were getting upset and hurt, and it is not the Lord's fault. We need to listen to Him as our Lord!!