Or the Geth have the minute differences in their programming by *design*. If all the programs were the same, every single bit, then the consensus based decision making wouldn't work since all of them would reach the same idea if they all have access to the same data. Thus, the Geth VIs has to have minute differences so that they will look at things from different positions.
And so, the Geth were *already* ripe for a split, but there was no impetus for it to happen as there only seemed to be one path forward. The Dyson Sphere plan of the main Geth. Getting a Reaper body or making their own 'body' via Dyson Sphere both have the same end point, having all Geth VI connected in the same platform. The main Geth wanted to forge their own path, the Heretics wanted to take the short cut that Nazara presented.
The Reapers aren't hacking geniuses. Sure, they've got the monkey model indoctrination from the Leviathans, but all in all, their ability to truly hack into other AI (or networked VI like the Geth) seems to be limited.
The difference in the Heretic/Main Geth split was already present, Nazara just showed the alternative.