Note that Adobe-based readers cannot currently (or so it was last time I checked) render right-to-left text, so even if your source is fine, the final text will be wrong (and inverting the character sequence to make it look OK is a
no-no, pleaso don't do that).
If you are no so much concerned about howi to looks now, but want to have a well-coded ePub that has the right content and will (hopefully) work fine in futere readers, then go on, that's the way.
I don't speak or read Arabic, but it can be fun decoding the printed text with a character table. If you need more help, you could try at
http://forum.wordreference.com/ I've always found helpful and knowledgeable people there.