Fr. McBrien (God bless him) is one whose writing is ambiguous enough that some people can claim that it says something unorthodox even if it might not actually do so.
However, the answer is that a properly informed conscience will never be in opposition to the authentic teachings of the Church.
Unfortunately some people assume that if there is a conflict, then automatically their 'conscience' is right, and the Church is wrong. Whereas in the situation of a conflict, the very first thing to do is to reconcile one's conscience with the teachings.
Now here's the thing. Suppose we have a person who is very anti-death penalty. Their state might permit it, and these people can legitimately say that their conscience does not permit them to 'accept' the morality of the death penalty, even though it is legal in their state, and even though it is not, per se, against the teachings of the Church. This is an example where a person could argue that his conscience demanded that he protest the death penalty even though if it is legal in the state, it is not strictly demanded by the Church that he protest. The person is not REJECTING Church teaching here.
Unfortunately, what we get more of is people saying, "Hey, I don't believe that we should deny marriage to gays, even though the Church says marriage is only between one man and one woman. My CONSCIENCE tells me that I must reject the Church's clear teaching and insist on gay marriage, and my conscience is ABOVE Church teaching and superior to it."
And **That is wrong. **A well informed conscience would acknowledge that marriage is between one man and one woman, and that no matter how much we may sympathize with our gay brothers and sisters, we cannot 'make' marriage into something between men and men, or women and women, anymore than we can 'make' the sun into a soap bubble or a violin. It's impossible to change what God Himself made (male and female, created to bring new life in marriage) and calling two gays 'married' doesn't make them married anymore than if my cat were to have kittens inside my closet that would make the kittens into slippers.
One's conscience here must align with the Church. If one still struggles, then one must acknowledge that the Church is correct, and that the difficulty is with the person who cannot (yet) bring themselves to understand and accept that fully.
I would imagine it would be the same with you Lutherans to a degree, wouldn't it? I mean, if you had a fellow Lutheran suddenly claim that, by golly, his conscience told him that Jesus was not 'fully God", but only a human being, and there was no way that he was going to accept the Divinity of Jesus. . .but he still insisted on being Lutheran, called himself a Lutheran, AND said that his point of view was totally all right and acceptable by ALL Lutherans and that if you didn't accept him you were a bigot and an antiLutheran yourself. . .you'd probably say that despite his 'sincere belief' he wouldn't be right and he'd either have to accept the teaching or stop calling himself a Lutheran, wouldn't you?