Dooku having a different colour like yellow or orange etc. would just be something new on screen which would be leaving the audience confused i think, Dooku as a rogue jedi wouldnt change his lightsaber colour purely just coz he has different views. I know the sith have red but that represents blood, death, danger etc. The jedi use blue and green to represent good. Dooku as a rogue Jedi would still see himself as a good person trying to do the right thing. It comes down to point of view. In a nutshell Sith know they are evil and they use fear as a advantage. Jedi are good that use colours that symbolise good like blue or green. Rogue Dooku would still use noble colours like blue or green because he thinks he is good.

Lightsabers and weapons and apart of the Jedi's soul in some ways. Lightsabers are not mood rings that change when they feel differently about something. If you were to change Dooku's colour would Anakin have different colour half way through the saga because he doesnt agree with the council? I think not.