Aren't Earisu, Aerith and Aeris all names, not actual words? Correct me if i'm wrong, but I don't believe there is a correct or incorrect way to pronounce (or in this case) translate a name. I could be wrong though, this is just what I believe!
Final Fantasy characters are far from easter eggs when it comes to finding them in Kingdom Hearts. Final Fantasy characters being in Kingdom Hearts is probably one of the great huge reasons that Kingdom Hearts sold big time. Final Fantasy helped Kingdom Hearts by practically selling out their characters to the game. Kingdom Hearts gained fans, Final Fantasy lost some- it was a trade, and all for money.
I'm not blaming Kingdom Hearts- the game, just the idea of it.
Names are words. エアリス (pronounced Earisu) and Aerith are the same name, Aeris is a different name. It's like saying Cloud and Clous are the same name. There is nothing wrong with pronouncing it Aeris if you want to (like a lot of people still call Tidus 'Tie-dus' even though they now know it's pronounced 'tee-dus') but her name is, and always was, Aerith.
Anyway, as for the whole Kingdom Hearts thing. I do agree that the FF characters there aren't very much in character, but I don't think it really matters. They're like cameos. I never really considered them to be the same characters, from the same story. Just like the disney characters, I don't think what happens and who they are in KH makes any difference to who they are and what their story is in their original movie. I just take Kingdom Hearts as a story of it's own, and the things that happen there aren't connected to the stories other characters come from. So in that way I don't think anything that happens could ever really ruin FF, because it's not FF, it's KH.