Yes they did, however parties or factions as the called them are human nature. People naturally group together around “a cause” legitimate or otherwise. I am afraid that concern of the Founding Fathers is one of the few times they engaged in wishful thinking rather a pragmatic clear-eyed assessment of human nature.
Biggest thing that would help is the hardest - repeal of the 17th Amendment. Give the states back their role in the federal government. That will be a hard sell!
I might feel differently about parties if we had developed more than two viable ones; I feel that dichotomizing political and social thought this way has only been bad for us.