This is where I have a problem. Giving Dooku a green or blue saber, when the rest of the jedi themselves have green and blue sabers pigeonholes him as a Jedi just as much as a red saber pigeonholes him as a Sith.

We need him to be more ambiguous than that, not only for the audience, but to make it more plausible that the Jedi believe he is a sith even when he's not.

I know it's just a colour at the end of the day, but it semiotically conveys a whole lot about the character, especially by association with the established sabre colour conventions.

We shouldn't know for a fact that Dooku is good any more than we should know from the outset that Palpatine is evil.