I think if you apply some discernment you will find there are those who say it is unilaterally wrong to judge the Church and there are those who say it is wrong to baselessly or unjustly judge the church. I would fall into the later, not the former.
I think you will also find most church-judging is not Church judging. There is only one Church; that is the body of Christ, the ekklesia (those called out of the world into service to God).
That is not the same as
congregations. The problem is we use the word, "church" to mean a whole bunch of things outside of scripture's usage. Those who judge
churches are not judging
the Church. Or at least they shouldn't be. Those who judge the Church are usually unfamiliar with the doctrine of
Church holiness and what
Christ's attribution on the Church means (they are often unfamiliar with the doctrine of Christ's impeccability, too, but that's tangential). This comes down to a fundamental difference in the respective doctrines of Ecclesiology.
Lastly, I think you'll also find that
conduct is what is being judged. Where the institution is being judged over a given group's conduct that is wrong.
And all of it is all the more wrong when it occurs absent any
evidence, which, sadly, is all too often and an indication that the judge is part of the problem to be solved. Hence...
Yes, that is called
hypocrisy and hypocrisy is something decried throughout scripture. That is always an indication there's something wrong on the plaintiff or judge's end of the matter.
Yep.
If it is any consolation they don't understand it, either.
There have always been critiques and there have always been critics. Much of the content in Paul's epistles is critical. He's spending a lot of time and effort correcting bad conduct. One of the most remarkable facts is that rarely does he treat any of these wrongdoers as if they aren't ekklesia! Similarly, the schisms and reforms that have occurred throughout Church history are all based in some form of judgment. Presumably the outcomes were each and all in God's hands.
Then there is the challenge of the restoration movements of the 1800s. These sects began preaching 1) the Church is corrupt and 2) therefore in need of restoration and 3) they're the guys doing the restoration, 4) so come join them. In time large portions of Christendom took on this view under the auspices of non-denominationalism even though almost every single one of the eventually formed a different denom (or cult), thereby further fragmenting the Church, which was they very thing they were purported resolved to address and solve. As more time passed certain branches of Christendom formed their theology around this premise the Church is corrupt. Certain unnamed groups even went so far as to say the Church was not supposed to be involved in influencing social and politcal policy and practice. This increasingly took a large portion of the Church out of the civic arena and it wasn't until Francis Schaeffer's writings and consequently Jerry Falwell's Moral Majority that this changed.
Now, fifty+ years later there's this raging debate between those who understand theology and Church history as I've just summarized and those who don't.