Hmm, I remember this remark from STIV:
"You'd think they could at least send us a ship. It's bad enough to be court-martialed and to have to spend the rest of our lives mining borite, but to have to go home in this Klingon flea trap?"
"We could learn a thing or two about this flea trap. It's got a cloaking device that cost us a lot."
"I just wish we could cloak the stench!"
Well, pardon me for being dense, but...if it's TRUE, how can it be prejudice?
If humans go aboard a Klingon ship and decide they don't like its smell or its quality (or lack thereof) of construction, then by definition it is not racism - it's direct personal experience. It's based on fact. To say "Klingons are ugly" is racism; to say that Klingons are warlike and brutal because you've seen them act that way on numerous occasions, well, I'm sorry but I don't see how that could be racist.
Kirk says he never trusted Klingons, and never will, because of his experience with them and because of David's murder. How is this racist?
(Burke and Samno, on the other hand? They were obviously racist. "They all look alike"..."You know only top of the line models can even talk"...those are clearly racist remarks. But those are just thoughts spoken aloud by two people, not representative of the entire crew.)
As for the lines in TOS about "freak": In one case, it was Kirk intentionally saying things he did not believe in order to 'bait' Spock into showing his emotions. And in the other, the crew were being provoked into irrational hatred by the "Day of the Dove" entity. So those are not genuine racist feelings in either case.