The story does not account for the Israeli raid coming just a couple of days after a North Korean ship docked in a Syrian port and transfered what ever it was carrying to the bunker site.
Something was in that shipment that made it urgent that the Israeli's to act quickly. Reactor fuel or parts for a reactor to be completed in years did not demand that urgency.
Whatever happened, you cannot discount its possible relationship to the failed Syrian Scud missile warhead loading in late July that killed a couple of dozen Iranian and Syrian technicians with what is thought to be posgene or VX gas. Was that to be a strike on Israel?
My guess is that this might have been an attempt to take DPRK nuclear material and turn it into a warhead, probably a dirty bomb, and....give it another try.
The threats have been flying for several years - the backers of Assad and Ahmadinejad may be getting restless for an actual attempt to "wipe Israel off the map".
I agree with your line of thinking.
For the Israeli’s to risk that kind of attack, perhaps they had intel that the “incomplete” facility was in fact made to look that way (straight out of Star Wars), and that the DPRK shipment was nuke material to get it going.