Venal, you are not a vast majority. If we're accustomed to red = bad guy, blue/green = good guy — which even if we've only seen TPM and AOTC up to this point we would be — Dooku wielding a red sabre is the giveaway that he's a villain. If you give him a different colour — any different colour — it's less likely to pigeonhole him as a simple villain in the viewer's mind.
Notwithstanding my defence of a yellow/gold sabre for him, I don't mind him getting a green one, provided the only other characters with one are Luke in ROTJ, Qui-Gon and possibly Windu if we're painting him as the unduly suspicious character that was thrown about a while ago in this thread, and all the other Jedi get blue.