As does the Times reporter, I read the report on an initial skim as being most critical of the university's procedures (or lack thereof) for investigating students' complaints about faculty misconduct. The report points to a number of adverse consequences of the ill-defined and poorly publicized grievance procedures. Reading between the lines, I suspect that one particularly frustrating consequence from the committee's point of view is that the absence of contemporaneous complaints and investigations made it almost impossible for the committee to determine the truth at this late date. Some of the most explosive allegations essentially come down to one person's word against another's (sometimes with two or three other witnesses on each side, but still a matter of whom who believe).
Hence the committee's description of itself as the "least bad" way to deal with the crisis once it had been allowed to fester for so long.
I found the committee's reaction to the three incidents it took most seriously pretty reasonable. The committee mostly relied on intuition and common sense, but its thinking struck me as indeed sensible. On the charge that a professor had ordered a student to leave the class after she made a comment that appeared to defend the Israeli military against charges of atrocities, I think the committee was right to think that the professor probably said something that was an improper reaction and that basically denied the student's right to question the professor's beliefs about Israel's conduct. And it was also right to conclude that it's impossible to tell whether that improper reaction included an order to leave the class (the student did not in fact leave the room).
I also found appropriate the resolution of the bizarre episode when a professor allegedly told a Jewish student that she couldn't have a claim to the land because she had green eyes and therefore wasn't a Semite. Especially given the context (a long after-class chat), and the fact that the student said nothing else happened during the semester to make the course exceptional in any way, I think the professor's explanation was very plausible: he said he sometimes uses physical features like that when arguing that claims to land based on one's choice of religion are absurd. Frankly, I'm not sure I understand his argument, and in particular his explanation of how the argument is illustrated by the difference between inherited physical characteristics (like eye color) and the religion passed down (non-genetically) from one's parents. Even in the written form in which he publicly defended himself, the argument strikes me as badly worded and perhaps pointless. But in the course of a lengthy and intense conversation, it doesn't seem unreasonable that he might have worded his argument in an even more obscure way or that the student might have misunderstood his meaning; and the accusation isn't that his arguments are wrong or incoherently explained, but that he actually claimed that he had a superior claim to the land because he had brown eyes and his interlocutor had green eyes, which strikes me as a much less plausible occurrence. [Note: this paragraph was updated from the original post after I read the professor's op-ed and realized that I'd misstated his position based on the synopsis in the committee's report.]
The unfortunate fact is that we'll never know the truth about most of the particular incidents that allegedly occurred. For that reason and others, there's no way this report will satisfy everyone, particularly those who claimed that the committee was composed of professors with overtly pro-Palestinian views. The organizations that pushed this issue will no doubt say--and, I think, honestly believe--that this is a whitewash and that serious misconduct has gone unpunished. But after reading the report, I'm not sure that it reasonably could have been any better.