The purpose of the comparison is quite simple: to illustrate that Wisconsin's commitment to free speech and the marketplace of ideas is uneven, at best. On the one hand, Wisconsin is willing to give a radical professor more rights than the law requires in the name of "academic freedom." On the other hand, Wisconsin appears to be willing to give Christians fewer rights than the law demands.I still disagree with him! If Barrett were trying to exclude non-Muslims from his class, the comparison would be apt.
The university perceives Barrett's classroom as furthering the marketplace of ideas, because he's given assurances that he will promote debate and treat different viewpoints fairly. You may find it hard to believe that he actually will, but the decision to retain him is based on that belief, and Barrett was required to give those assurances.
The student group, as I understand it from reading French's piece, is seeking the right to discriminate against other students in order to preserve its ideological character. That may be a worthy pursuit, and the university may be wrong to reject it, but it doesn't demonstrate the university is being inconsistent. The university's decision is aimed at preserving diversity and debate within the group. I understand the argument against this. There is less debate overall if groups can be diluted with members who disagree with what they stand for.
I'm not saying the students aren't right, just that French hasn't identified hypocrisy.