Industrial flash (LED?) for rolling shutter
I'm not quite sure I understand the issue, but I'll take a stab at it anyway.

I'm assuming you can get a light source that you can turn on and off with digital logic, and your problem is that the flash sync signal isn't long enough to keep the light on for your image acquisition.

If this is the case, just use the flash sync to trigger a monostable multivibrator (i.e., a one shot) with a pulse long enough to allow the image capture, then use the output of the one shot to turn on your light source.

Not sure you can achieve the same functionality with the Pi alone.  It would be simple on a microcontroller with full interrupt functionality, but then you lose the imaging and file handling convenience of the Pi.  You might consider a Beaglebone Black, which has its own microcontroller (though I haven't read much about using it).

In any case, the one-shot is a one-chip circuit, and shouldn't be burdensome to implement.