Some would say the episode Zecora was first introduced was "suggestive" in the manner in how they went about portraying her. Honestly though, look at it through the eyes of the ponies not through the eyes of someone that digs into conflicts and deems them racist or not based on the stereotype of society. (What I mean is, let's just take the show for what they intended it to be toward the ponies, not what people make it out to be. Even if the creators implied some kind of darker side to this, just take it how it is, not how you want it to be.)
If we look at this situation through the eyes of Ponyville's set standards and evaluated the situation the way the ponies would instead of how we as people evaluate similar things in our everyday lives, we'd see this conflict differently. How? Well, I'll explain.
To the ponies, (or how it was made to be in the show) they had never seen anything like a zebra before and the way she was acting definitely put a damper on their opinions. Obviously all this should be very simple to understand considering that is what that episode's lesson was about, but I reiterated it just in case someone didn't catch it. Also to the Ponyville citizens, the possible risk that Zecora was into some type of magic that was supposedly of the "dark" category may have put a damper on some things as well. They just were afraid of what they didn't know. I mean come on, everyone is a product of their environment until they expand their realization of certain things. So can you blame the Ponyville citizens for acting the way they did? Maybe (depending on your opinion) But on another hand, it was just to protect themselves, but honestly they did over-react. Now obviously after either watching this said episode or reading what it was about, you'd know the moral of the story was to not judge a book by it's cover, but sometimes I'd say it's okay to. Now what do I mean by that? I'd really lean towards treating everyone equally until proven otherwise. So yeah, in a way the ponies heavily over-reacted towards Zecora when they just should have played it out as it was just another pony. I can understand both sides of the story, but is it racist? Not at all. There is no way the ponies were judging anything by race or species in this episode. Now, how could you say the show intended for it to be "racist" when the characters can't even generalize the situation as a discriminatory whatsoever?
The episode was what it was. The ponies were afraid of something they didn't know/understand so they hid. Just because it was a zebra that did "black magic" doesn't mean a thing because you know darn good and well the ponies didn't even know how she talked or acted other than what they saw. So is "racism" a possibility? Not at all. I mean come on, they don't even have racial classification in Ponyville... Just species and mythical creatures.