You need to be using the correct font in order to have the accents show up. There are different ways of encoding Greek.
For something like this, a PDF file, with the correct font embedded in the file, is the most "hassle free" solution. Since Mobi does not support font embedding, if you create a Mobi file, you need to have the correct font on the reading device. Some devices allow you to add your own fonts; others do not.
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