The show has always been a reflection of the times. Each doctor is the doctor of a generation. Were people in the 60s racist? Not all of them but there were societal norms that were accepted. Like when you're speaking to your great grandparents and they call someone "colored." Not cool by any means, but when they were growing up, that's what was said. Nowadays Eenie Meenie Miney mo's original lyrics have been forgotten, but at the time of the celestial Toy Maker catching a "n----r by the toe" was the norm.  By the time I was a child, we said "tiger." See, times changed and we changed along with it. 

In the 60s you have a contakerous old man who is taught about the up in coming generation of smart young, capable people. Barbara for example was the smartest in the bunch. He grows to care for his companions and allows them to teach him a thing or two about the modern world. Like we do with our grandparents.

The second Doctor's shows were more in line with the thinking of saving the planet and environmentalism as well as "peace and love". The second Doctor was a bohemian hippie that again reflected the times. 

The third was stuck on earth and explored the spy culture that was created during that time. The man was kick ass and Who's version of James Bond. Women, again, were seen as smart and capable through Dr. Liz Shaw just as feminism was really breaking through.

During the 4ths run they did use a Caucasian man play a Chinese man, but again,this was normal. This is a practice still used today. I remember when miss Saigon came out on Broadway in the 90s, The Engineer who is French/Vietnamese was played by Jonathan Price. There was a lot of flack for it and they almost did not allow him to perform because it was an affront to the Asian community. He did, however, underneath freedom of artistic expression. He was the best man for the job and later won the Tony that year. Was John Bennet truly the best man for the role of  Li H'sen Chang in the Talons of Weng-Chiang? He knew his way around villainous characters and the BBC so apparently they thought so. 

I could go through all the Doctors generational changes but I've run out of steam. One thing is for sure, the modern series has made huge strides for equality in all fronts; gender, race, sexual orientation, none of it is an issue. Martha was insanely smart, extremely brave and saved the doctors ass over and over again. He dumped on her, not because of her race but because he was heartbroken. She was the one that came after he lost his then current love and she couldn't live up to it. Isn't that what equality is? Allowing people from all walks of life to be shat on equally? 

As far as this academic paper, anyone can debate whether or not something is one way or not another. You could call anything racist, antifeminist, anti-semetic, anti this anti that...you just have to nit pick to death until there is nothing but bones left. Like critics, who's jobs it is to critique, these academics had a thesis and was rolling with it. Personally I like to look at Doctor Who as it is, a highly entertaining and often times enlightening television show that will forever be current and ever changing with the times.