He did have more planned out than they did for any of the sequels. His emotional dialogue sucked but he did create an overall coherent storyline. And Jar Jar’s actor claims that the plans for Jar Jar did change after Lucas saw how unpopular he was.
Maybe the plan was just for Jar Jar to be force sensitive, which would explain some of the coincidences with his character. Except for the clumsiness, which doesn’t really fit with any force sensitive user. Unless it was an act.
But, one scene in TPM doesn’t fit with him being a secret Sith: when he gets his hand stuck right before Anakin does a test fire of his pod racer. Padme was the only one to even notice and it seemed like a dumb gamble to come close to dying to give further evidence to one character that he was a bumbling idiot when they all already thought that.
Also if Qui Gon had no trouble using the force to influence Boss Nass, why wouldn’t Jar Jar do the same? Unless leaving the Gungan city itself was suspicious and he needed an excuse to be away.
I used to be convinced about this, but at this point I don’t think there’s any way to know unless Lucas himself comes out and says it. The evidence is too ambiguous and the change to Jar Jar’s character could have just been “move him to the background”.