The Vatican said that the Pope had been misquoted and since the episode, several of the professors have retracted their protest.

Let's clarify this sentence a little bit: The Vatican said that the Pope had been misquoted, and the Vatican said that several professors have retracted their protest since the episode. The link reporting this statement is to a press release from the Catholic News Agency, which names only a single professor out of the "several" that retracted. A recent interview on NewScientist (sorry, non-free subscription required) with one of the leaders of the protest suggests a different story, that support for the protest has increased since the event:

Only 67 of us signed the letter to our rector, however thousands of people are now supporting our initiative by signing online documents. What worried me was the reaction of the Italian media, commentators and even left-wing politicians. Their only argument was: these people are intolerant, they shut the pope's mouth. But the pope is talking continuously. It is we who have problems putting across our arguments. The church operates colleges and university centres all over the world. It owns radio and TV stations, newspapers, magazines.

This interview also mentions that the Pope's speech was read at the opening ceremony anyway.