Funny thing, I was also thinking about Mill's "On liberty" when reading this thread. I believe the issue is deeper:

In politics you often have a winning side and a losing side. The winning side can use various techniques to silence the losing side. People sympathetic to the losing side will move to meta arguments about why it is wrong to silence your opponents. -- The unfortunate, but logical, consequence is that arguing about why it is wrong to silence your opponents becomes an evidence for belonging to the losing side. An automatic status hit.

Therefore, it was easy to interpret Mill as an advocate for losing side of his days; and it is also easy to believe that he would support the losing side of today (at least indirectly by his meta arguments) if he were alive today... if what you know about him is that he argued that it is wrong to silence your opponents instead of debating them (which is a part that impressed me strongly).

If Mill advocated that even people guilty of the horrible crime of atheism should be able to publish their opinions, even if just to increase the quality of the theist arguments against them... it seems logical that today he could say the same thing about people guilty of believing in differences between people, or similar stuff. (Of course this assumes that he would be consistent in his beliefs and willing to bite the bullet.)

The problem would not be with Mills beliefs per se, but with inferences people would make from his meta arguments. And he would not even have to support the low-status people to create this association; the low-status people would create the association by quoting him often. -- And then he would have to choose between implicitly denying his support to them, or being considered a silent supporter.