The 'flags are not languages' thing gets repeated a lot and it certainly has a valid point. But it shouldn't be taken as an absolute law. Flags are not languages but users do associate a French flag with the French language (for example) and so will be drawn to flag pictures as a way to change the display language.
In the case of something like setup for an OS, big international software, then yes, flags are wrong. But if you are for example making the website of the Moscow branch of the Turkish-Russian Friendship Association then flags are totally appropriate and fit in very well with the feel of the site (though they could well get lost midst the million other flags that would be seen on such a site!).
In my experience testing with Irish users nobody really has any problem when people use the British or, rather more rare in Europe, the American flag for English, they get what it means just fine and it helps them to navigate, which is the core point of usability (though when the British flag for English is coupled with the Republic's flag for Gaelic...then things get silly. I've no idea what those designers were thinking.).
If you really must use a flag- the Arab League has a flag, that maybe?
Though in this case it sounds like you are going for a very global program rather than a more localized affair (its not the Saudi embassy in Rome) so flags are not the way to go. By the sounds if it there would be so many of them that it would look rather messy anyway.
I'd suggest just going with Arabic written in Arabic with (Arabic) or / Arabic in English (or whatever the currently selected language is) next to it.