The idea in season 1 was that Rittenhouse was already everywhere, controlling everything, secretly ruling the United States for centuries and shaping world events from behind the throne. They didn't need to change history because they'd been making history to suit themselves for 250 years or more. It was a huge retcon in itself when they were shown to be nominally brought down by the authorities in the first-season finale, because up until then, we'd been told that they already were the authorities, essentially -- that they controlled every agency and there was no escaping their all-seeing eye. It was your classic self-contradictory conspiracy story where the conspiracy is so ubiquitous and all-powerful that it has no reason to be secret because it already runs everything. So they've had to retcon Rittenhouse into something less pervasive in order to generate a plotline about trying to stop them from becoming pervasive. It's a complete revision of the core premise.
Besides, none of this addresses the logic hole I was talking about. If they put sleeper agents in the past centuries ago, then logically those agents would have already changed history centuries ago. Whatever they were put there to do would already have been done hundreds of years before Lucy and the others were born. So the timeline should already have been changed.