Well, they said they didn't want a factional system, then they built rules which guaranteed two factions, modelled directly after rules which had done the same elsewhere, and all while organizing themselves into two factions which were visible in nascent form in the first national elections under the Constitution and well solidified by the time Washington was to be replaced as President.

So, do you listen to their words, or their actions? The founders were, to all evidence, a lot like politicians of today, publicly cursing the ills of partisanship while deeply engaged in it, mostly as a rhetorical device against the other party.