For a clear-headed discussion of academic freedom in the context of the John Yoo case, see here. I have a few of additional things to say on the matter.

When people typically argue that Yoo should be fired, they tend to resort to two main arguments.

The magic job title: Suppose you and I strike up a conversation, and you happen to ask me what I think about the power of the executive, and I reply that since the president is the commander-in-chief of the US armed forces, there is no legal limitation whatsoever on the orders he can give to the troops. Interesting, you say, can you write this down for me along with the references? Sure, I say.

That's just talk.

On the other hand, suppose I have a JD and have "white house legal counsel" as my job title. Further...

...Suppose you and I strike up a conversation, and you happen to ask me what I think about the power of the executive, and I reply that since the president is the commander-in-chief of the US armed forces, there is no legal limitation whatsoever on the orders he can give to the troops. Interesting, you say, can you write this down for me along with the references? Sure, I say.

Well now thats a war crime.

According to this view, writing down my opinions is clearly not a crime. Its my JD and my job title that magically transform writing my opinions into crimes.

And that, of course, is just silly - a lawyer is just someone who writes down his opinions in exchange for money. Nothing more, nothing less.

The consequence argument: A consequence of Yoo's writing down his opinions was that people were tortured, and therefore Yoo is guilty of a war crime. For example, Marty Lederman (an actual law professor - I am not just pulling random yahoos of the internets) writes,

...no one thinks a professor should be fired for having views deemed morally reprehensible or for producing a shoddy piece of work. The claim here is that the morally reprehensible views, and the shoddy work, in this case were put to use in official state conduct that facilitated and immunized horrific crimes. And that makes the question at least a bit more complicated...

Of course, nothing in this argument references the fact that Yoo was a white house legal counsel. In fact, if he just expressed his views to Bush over lunch, the argument would still hold. As long as his act results in torture or, in Lederman's words, is "put to use in official state conduct that facilitated and immunized horrific crimes," there is no difference whether he wrote it down in a memo or expressed it verbally.

Nor does he have to express it to Bush; it could be any kind of lower ranking official in the white house. Nor, come to think of it, would Yoo even need to do that; if he just published the arguments of his memo in a magazine, the effects would be the same.

You can see how this argument leads to a blanket restriction on speech. Once you start saying that some speech is a war crime based on the acts it inspires in other people (irrespective of its content - for this argument to work, it doesn't matter if Yoo is right or wrong!), free speech is pretty much in the toilet.