I consider then harmful.
I suspect Emoji are like those smileys with mustaches, beer steins, and birthday cakes that show up in skype chat. I hate that garbage. Many a time, I write a sentence that contains a parenhtesis, using grammar correctly, and then my message comes across as some random retarded shit sprinkled with smileys. I have a hard enough time avoiding typos, I don't really need the client mucking it up even worse.
That's not the fault of Emoji, that is the fault of the client replacing things like ":)" and ";P" with pictures in order to simulate Emjoi.
As bizarre as it sounds, you actually want to be embracing the support of Emoji! This is because all the searching and replacing logic (which, as you rightly pointed out, tends to make unwanted changes to your text) is now redundant and can be removed by the developers.
The net result is that people can still insert smileys with moustaches, beer steins, and birthday cakes and you can still type grammatically correct messages (or code) without fear of them being replaced with pictures. A win for everyone.