Beliefs and Politics

As an editor, it can often be difficult to separate out the different levels of criticism that are appropriate.
I work for people--working on helping them express themselves and their ideas clearly. And it is not my role--as I have chosen to define it--to try to change their ideas. I work for academic clients--the whole point is that they are generating the ideas. This is unlike an editor at a publishing house or a newspaper whose concern is to make sure that all writings meet the editorial standards of the organization.
But sometimes I don't agree with those ideas.

And then a conflict ensues: at what point does a poorly expressed argument become just a poor argument?
I try to separate the premises from the conclusions.
The premises have to pass one of two tests: either 1) I think they're sound and academically defensible on their own merits, or 2) they are supported by some outside authority.
When it's the second, I can have problems.

For example, working with Freudian theories is difficult. It's not that I've ever studied Freud extensively, but ideas like penis envy or the oedipal complex--ideas that are presumed to be true for all people or all of one group of people--such theories strike me as highly problematic--they reduce the complexity and variation of human experience to a single model--and, in Freud's case, these ideas often involve specific important experiences--e.g. the "primal scene", in which a child sees/hears his/her parents making love--that may not happen to everyone.

Nowadays, of course, there are plenty who reject many aspects of Freudian thought--but what about working with those who do accept it?
I think Freud's logic is problematic--he uses inductive logic in an inappropriate fashion--from the cases that he studied, he extrapolates to all humans--or perhaps those who use his theories extrapolate from his case studies to all humans. And that just ain't good logic.
It's not good science. As Karl Popper points out in the Logic of Scientific Discovery, induction cannot be used to prove a point--it can only be used to disprove a point--No matter how many white swans you may see, it does not disprove the possibility of a non-white swan.
This is the principle of falsification that has led to the use of null hypotheses is science annd statistics--once you disprove the null hypothesis, you are free to suggest an alternative hypothesis that has not been rejected.

But how do I break the critique of Freud's logic from a critique of a work that uses Freud as a premise?
Despite my dislike of Freud's logic, I don't want to reject work that accepts his theory--that's not my business. But I do want to keep that work from doing things that might get it rejected by a faculty committee or a peer review board.

It's an especially situation if I attempt to critique the structure of an argument and that is perceived as an attack on the premises or the conclusion of the argument itself.
Sometimes I can't quite be sure if I have been attacking the argument, not the structure of the argument.