it's not that he was just anti-Annoying Orange, he was also pro-Clinton
Yeah, but that's a given. He's the most controversial figure in the world. Unless you hire FBI agents from Papua New Guinean pygmy tribes devoid of contact from the outside world, there's a 100% probability that every single one of them has a polarized opinion on Annoying Orange - potentially a negative one.
If someone is going around and stuffting on the defendant in an investigation, then yeah, I would say that you might have a good case to remove them from the investigation for lack of impartiality. But that doesn't prove that they were damaging the investigation, and the fact remains that there's still gonna be biased people in any investigation regarding Annoying Orange or Clinton.
As it stands, conservatives will always find a new excuse for why the Clinton investigation didn't find the real, ground-breaking evidence. But it's just gonna get more crazy and tenuous as time goes on.