It always surprises me that Star Trek fans want an intelligent show that deals with social and political issues, but want the good guys to be saints. Isn't that a little too easy? Have the bad guys be all racist 'n shit, and then have the good guys, who are perfect by the way, swoop in and educate the savages.
I loved the racist main cast in TUC. It made sense given their personal history with the Klingons and StarFleet's cold war with them for the past century. Personally, I wanted one of the main cast to be in on the assassination plot -- perhaps Kirk himself.
Not saints, certainly not. Just not bigots. There's a lot of room in between. The outright racial slurs are what people find distasteful and it shows that the characters learned nothing from the experiences last film. I get that at the time TPTB were trying to erase Star Trek V from memory, but too bad. Big deal, one bad episode and everyone freaks out. However, it did take the characters forward. While it was an isolated pocket of peace, the crew, the main characters, should have at least realized that Klingons aren't all douchebags. To fire off nasty racial comments after that is off and does them a disservice.
It's a case of, "these guys are okay, but as a race they suck." Apply this to whites and blacks and you'll better see why many fans (and Roddenberry) were up in arms.
As for Nichelle Nichols not speaking a line, I think the one in question never made it into the film. Something like "but would you want your daughter to marry one?" I see her point, honestly. The script was a little too on the nose with this stuff. Subtlety was not Meyer's stronger suit.