The biblical practice of naming people is either to warn others against them (e.g. 1 Tim. 1:20), or to academically discuss the views of another. In other words, naming names should be intentional. The question about naming names when discussing issues then arise.
The fact of the matter is: where there is no necessity of naming names, names do not have to be mentioned. When discussing various issues, if the intention is to discuss doctrine and practice, there is simply no need to name churches and ministries if they are not intentionally adopting heretical positions. If said churches and/or ministries feel in some sense slighted by critique, well ... if the shoe fits, wear it. That the focus is on any particular doctrine and practice, not on any church, is an indication that the critique was never meant as a personal attack against any particular church and/or ministry that are not named.
Previously, I had been flamed for naming names. Recently, however, I have been criticized for NOT naming names. It is indeed a strange day, when people expect me to criticize them personally by name if I happen to criticize a doctrine or praxis they hold to. Do they or do they not know the difference between criticizing said doctrine and/or praxis, and criticizing churches/ministries that hold to said doctrine and/or praxis?
As far as I am concerned, when I critiqued doctrine and/or praxis "in the abstract," that means that I am not treating those who hold to it as intentionally in error. In other words, such critique is meant to be alongside those (not named) who hold to such positions, not against those who hold to such positions. It is to say, "Look, I care about you. You should not believe position X, because..." Do people prefer to be seen as the perpetrator (knowingly or unknowingly) of error to be opposed?