How do I remove the stroke overlap between the individual Arabic characters when I use zero fill or even white fill?
There's no need to outline your text. Set the stroke and fill using the Appearance panel (Window → Appearance) and drag the stroke to the bottom so that it is behind everything else.
If you're happy with a solid fill then you're done.
If you want a transparent fill then set the opacity of your fill to 0 (with a solid color fill, not a transparent fill) and check "Transparency Knockout Group" on the layers transparency options.
Note, this has nothing to do with Arabic text and the same problem exists for any script.
Add a white fill to all shapes then go to Pathfinder -> Unite then remove fill if you feel like it.
This assumes you are treating your text as artwork. If the text is still editable, right click on it and select Create Outlines and only then do the above.