With regard to excommunication, I don't think anyone necessarily disputes the church's right to exclude people from among its ranks for publicly questioning it. Mostly, I think, people are just lamenting the fact that it has become a place that finds it necessary to do so. It used not to be this way. The church has altered significantly since the 70s when I grew up. It has gone, metaphorically, from an "employee owned and operated" enterprise to a strictly hierarchical command-and-control model that, it appears, brooks no insubordination.
Also, we obscure much when we say "the church does this" or "the church does that". Churches are not animate objects that "do" things. What this type of speaking obscures is the fact that WE are the church. If there's any doing of deeds, it is people who are doing them. In this case, what it boils down to is that some people in the church are deciding to kick other people out of the church.
The people ordering or doing the kicking out consider themselves authorized and justified in do so. Perhaps they are. We all understand how the church is set up. "Mine house is a house of order, saith the Lord." And in this house of order, power and authority flow, in one direction only, from the person at the top of the org chart, through various intermediate layers, and finally down to the worker bees.
It is generally assumed that the source of that power and authority is divine. Perhaps it is. But perhaps it is more accurate to say that the source of power is really people's *belief* that it is divine -- a subtle but important difference.
Either way, the hierarchical nature of the church makes it impossible to tell the difference between what is actually the Lord's will and the personal agenda of someone authorized to act in the name of The Lord. Of course we always have the option to ask The Lord directly for a testimony that a church leader is acting properly, but note that it is never, ever acceptable for the answer to be "no". And so, there is no way for people lower down the hierarchy to discover and remove corruption from a location higher up. Such an action, if it ever comes, could only come from above in the hierarchy.
However, we have learned as a people, through hard experience, the immutable law that any governing structure really derives its legitimacy from the consent of the governed. In the case of the church, this takes the form of belief on the members' part that The Lord is in control. Regardless of whether that's true, if the members suddenly ceased to believe it, the orderly hierarchy of control would cease to function.
And belief, it turns out, is a precarious thing to maintain in these days of Information. So the hierarchy, in order to maintain its legitimacy feels compelled to act when threatened by the prospect of unbelief. That is why public disagreement becomes an excommunicable offense.
The problem is that the sword of excommunication, which at one time could be wielded with impunity, is no longer the tool it used to be. The people in the hierarchy of control now run the terrible risk of appearing to be a self-serving organization interested only in maintaining their position of power. If a critical mass of the church members were to place such an interpretation on this event, who knows what the consequences would be?
In any case, "the church" is stuck between a rock and a hard place. The legitimacy of the strict hierarchy of the church is increasingly imperiled by the free flow of information. But to decentralize is also not without significant risks. Since the church -- any church -- largely exists because of the willing belief of its members, it must tread lightly lest in its efforts to maintain order it cut off too many valiant members who also happen to be independent thinkers and/or can't fit into the sanctioned gender molds.
Far better in the long run, I think, to expand the tent even at the risk of offending its hard-core base. Of course it is precisely that base that is in firm control right now, so that will not happen easily. But we have seen what pressure can be brought to bear by people voting with their feet. I hope things turn out for the best.