The thing that you need to remember out Twilight Sparkles magic powers is that her talent (and all ponies have talents, reflected by their cutie marks) is her skill at magic. We see this when casts a spell on Rarity that gives her wings, which despite being a unicorn, Rarity is incapable of doing. I think that the extent of a unicorns magical powers is tied to the talent their cutie mark reflects. So while Twilight Sparkle can cast almost any spell or perform any task with her magic because her cutie mark signifies talented at magic, Raritys powers seem to be more limited to things that help her with her talent of fashion designer like fine control over tools like needles and scissors and the creation of light shows.
I think this is why unicorns cant simply take over the businesses earth ponies run with manual labor, because their magic has limited abilities outside of their cutie-mark talent. In reference to the apple harvest, while Twilight Sparkle is able to harvest a large amount of apples using magic I imagine most unicorns would be incapable of that feat, and would probably become fatigued quickly. Also, even if a unicorn was able to harvest apples faster than an earth pony, their magic would probably not give them greater knowledge or skill at maintaining the apple orchards. All of the apple orchards of Equsteria seem to be run by one family whose cutie marks are all of apples, reflecting their special talent at cultivating them. Even if a magically superior unicorn would try to go into business against the earth pony Apple family, she would probably fail without the proper cutie mark.
Also, it is possible that cutie marks are hereditary within families, as shown in the Apple family and their apple-based cutie marks. It would also explain why the ponies names frequently match their cutie marks, because their parents were able to make an educated guess based on family history what their childs cutie mark and special talent would ultimately be. So if the cutie mark that signifies good at cultivating apples is restricted to earth pony families, a unicorn would be unlikely to have one and create a magically superior apple cultivation business. In that way the inequality that would seem to arise between earth ponies and pegasi and unicorns would be dampened, because while unicorns control magic and pegasi can fly and control the weather, earth ponies would have a wider variety of cutie marks that unicorn/pegasus families dont have, and thus would be much more talented and capable at those tasks.
So in short, even though only unicorns posses magic, they cannot control all aspects of society with that magic because their magical abilities are only powerful in the areas their cutie mark-talents require it to be. Because earth ponies have a different set of cutie marks and thus a different set of talents than unicorns (and pegasi) they all work together on equal footing because Equastrian society could not function without the talents of all of the different types of ponies working together.
