I thought about that too, but I speculate that the clean versions from Siemens wouldn't come from the factory ready to run an Iranian nuke plant -- you'd think that code would all be developed by the engineers who run the plant. All of that code would have to be recompiled from source too, as Stuxnet attaches itself to the PLC binaries.
That's certainly possible, although I don't understand why they would take that approach. The PLCs themselves should be relatively standardized, and any specific software that was created in house should be in an offline backup somewhere. Clearly, they didn't follow best practices, but it shouldn't take a year to start from scratch, assuming you had the basics on file.
Of course this is all wild speculation.