Focus on the House Church:
Contrary to the position of many modern Church leaders, the reason that bad things happen in Churches isn't because “we need to get back to holiness”, i.e., focus without reflection on endless strict rules.
The reason for some types of problems is that what people refer to as a “Church” is often a public venue.
I've come to the firm belief that a Healthy Church is a House Church and that there's no two ways about it.
Once money and real estate get into the mix, things can go bad quickly. I can't say for sure that it's out of bounds to set up a Church as, for example, a non-profit organization, but I feel that it's a mistake.
Individuals or groups of people could safely make an organization that gives to the poor or to spreading the message of Christ.
However, once you equate that organization with the identity of a “Church”, you're buying into a falsehood. The falsehood is that “a Church” is a thing other than a group of people who are called by God.
The Church as a public venue, as a business, even as a non-profit, is something different.
If you operate a Church as a public venue, you need to take everything which goes with that.
Attendees may be there to learn and to grow in a spiritual sense. Or they may be there to signal virtue, to manipulate and profit socially or financially, or to victimize. Sexual abuse, for example, isn't uncommon.
Do background checks. Don't assume that a “Christian” education or “correct” doctrinal statement means that a person is “good”.
Regular Churches often cling to tradition as though it has something to do with the Bible. For example, Creflo Dollar refers to house Churches as “weird little churches”, citing the fact that Jesus went to the synagogues to preach “as was his custom”.
However, note that Jesus was there to pull people out of a system that he was saying was corrupt and that Jesus himself started a house Church. Each of the members in turn started house Churches.
If you're in a regular Church and you notice that a group of people is moving towards independence, understand that it's time to plant a new Church and let it grow as a seed does into a new and healthy tree.
It's not appropriate to cut down saplings of this type. However, in my own life, I've watched Calvary Church of Souderton do this at every turn for the past 20 years. Other Churches have exhibited similar behavior.
I've been attending house Churches even before I knew that I was. I went to a few different Bible studies that became independent. These groups were independent in many ways even when they were sanctioned by regular Churches.
For those who are familiar with 1BC (First Baptist Church of Perkasie), there's some related 1BC discussion at this link.
Organic church books and house church books cover these topics in detail, and most I've seen more or less agree with a participatory meeting rather than a top-down managed function where there are “clergy” and “laity”.
Such a flattened model is more Biblical given what I've said above. With this model, there are several key benefits. One is that the Bible suddenly applies to you! You don't have to “apply it to your life” because the advice in the New Testament doesn't already apply to your life applies directly to house churches.
You will still have problems, but at least you'll have the problems the Bible addresses: people arguing over food, people knowing about and overlooking immorality, elitism, too many people ministering too much, trying to promote following the Mosaic law, people speaking in a language people don't understand without an interpreter, doing that type of talk for pretend (“babbling,” or what ethnographers studying cults call ecstatic speech; “tongues” is never a general vague term in the Bible except when describing misuse), etc. Since the Bible addresses such problems, it will be of great help to you if you move to the organic church model.
You can see how Christ works in an uncontrolled environment instead of putting all the power into human hands out of fear.