He was, but Sidious clearly manipulated him to do it. There’s even a chapter in the Aftermath trilogy where Jar Jar is shown as being an outcast for unwittingly allowing Sidious to rise to power.
It’s extremely likely that neither JJ, KK, or Rian read Aftermath, or indeed most EU books. Maybe they read a wiki summary at best.
The directors and Disney in general don’t really care about the canon as much as the fandom does. Pablo probably has a headache with every new script that comes out as he has to explain the latest contraction.