Thank you for providing a link to your source. I see that it has been misquoted slightly. The source material in your link actually goes like this:
The choices we make typically reflect our desires: we choose what, all things considered, we want. According to the conventional view, the process by which we make choices is rational. We consider the pros and cons of a particular choice or maybe even do a more formal cost-benefit analysis. After weighing our options, we choose. For the most part, it is a process carried out in our conscious mind.
A growing body of evidence suggests, however, that many of our choices are not made in this fashion. We do not make them, if by “we” is meant our conscious minds. To the contrary, the choices are made unconsciously, and it is only after they have been made “for us” that we are informed of them, at which point we put our stamp of approval on them.
Here, I've used boldface to point out the differences between the original and your transcription. For the purpose of answering your question, the only important change is that "We" is italicized in the original, indicating that the author meant "the word 'we'" or "the concept of 'we'".
Frankly, I am not comfortable with the construct "by 'we' is meant", and changing the verb to "are" doesn't fix it. I prefer these:
1: We do not make them, if “we” means our conscious minds.
2: We do not make them, if “we” is understood to mean our conscious minds.
3: We do not make them, if “we” refers to our conscious minds.
The singular verbs "means", "is", and "refers" work in my examples if "we" is understood to mean "the word 'we'" or "the concept of 'we'", either of which must be seen as a singular subject.