Yeah, if Dooku wasn't really evil, it would probably leave Obi-Wan asking more questions about which side Qui Gon would have chosen. There's not any way to directly convey that in the movie, but it's part of something wonderful called SUBTLETY, something which the prequels could stand to use more of anyway! Also, another reason a green lightsaber would be great for Dooku is that it'd reinforce his connection to Qui Gon.
I really like the idea that Dooku isn't really evil-- he's an idealist who sees the corruption in the Republic, and is trying to do something about it. One question though: would the connection between him and Sideous be removed completely, as in the scene where he meets up with Sideous at the end is gone? I have mixed feelings about it. On the one hand, it would show that Dooku is playing both sides, which keeps his true motives a bit more ambiguous. However, on the other hand, if he really is an idealist it's possible that he under no circumstances would lower himself to working with a Sith, even if he's going behind Sideous' back. I'm not really sure which way it should go, but also I did like that there was some foreshadowing to the Death Star in Episode 2 (though I do feel like showing its construction in ROTS was unnecessary and chronologically sloppy).