As vim is not BiDi enabled this should not be possible.
But I've been fiddling around a bit and it seems that vim + Konsole (KDE's terminal emulator) seems to do the job if you enable bidirectional support for Konsole. In vim (NO arabic options enabled) you should be able to write LTR and RTL, but letters will always be in isolated form (no shaping). I've found that setting the 'arabicshape' option then unsetting it seems to fix that. Short vowels are not displayed correctly, even though they seem to be written just fine to the file.
I have not tried with other terminal emulators, I'm not aware of their BiDi capabilities. Gnome-terminal maybe ?