So is there a real justification for separate alphabets here?
To my mind, yes.
It's worth noting that Aramaic can also be written in the (encoded) Syraic script, and my superficial googling suggests that at least one currently-used form of Syraic dates back over two millenia.
-- Curtis Clark http://www.csupomona.edu/~jcclark/ Mockingbird Font Works http://www.mockfont.com/
