You are 100% correct.

I see Lord Jesus as having modeled and taught tolerance, acceptance and inclusivity in some ways but not in all. It is therefore very important to be careful to avoid over-generalizing, such as the false idea that says, "as followers of Lord Jesus, we should be tolerant and accepting of all things". There's a very true cliche that goes something like, "love the sinner and hate the sin". The Lord was kind, loving, tolerant and forgiving towards the woman caught in adultery, the woman at the well and others, but was not at all tolerant of the hypocrisy within the prevailing religious system. Another false and much propagated statement which i believe embraces the same line of reasoning is that "we should not judge" a partial passage taken out of context which cuts out a substantial portion of what Lord Jesus was teaching there.

One point i believe you are making and with which i agree is that too often many within mainstream christianity and the accompanying church system follow after the wrong model and act too much like the Spirit quenching religious pharisees and not enough like the Spirit filled and Spirit led Lord Jesus. The reasons for this may be numerous, but i believe a big part of it is that people in many ways are following after a religious system more than following after the Holy Spirit / the Living God / God's living voice / the tree of Life for themselves. Sounds familiar, right?, like maybe what the pharisees and their followers were doing? Indoctrination into the ways of the system is a form of groupthink and there can be a lot of peer pressure to conform to this for anyone who wishes to fit in. If a pastor (who becomes so revered in many situations and actually becomes an idol to many) is off the mark in one or more important ways, (including something so important let's say as not walking in love), but those hearing him do not have the wisdom and/or courage to discern for themselves,... or are awestruck by his perceived greatness and trustworthiness... they will be taken in by his false teaching and false example and will likely begin to incorporate this into their own expression of their christian walk.

Of course a very costly mistake can be made by being too tolerant and accepting of sin including the very kinds of hypocritical sin in which the leaders within the religious establishment 2000 years ago were immersed, a model which many within the religious establishment today have embraced for themselves.