My instinct is to remove Gunray and other Neimodians entirely in order to paint a picture of Dooku as a good guy, but at the same time, the Jedi need a reason not to trust him, and associating with Gunray is certainly a reason after the whole Naboo thing.
The only gap in logic is why didn't Dooku go to the Jedi with his suspicions in the first place? Why start a war first before telling an imprisoned Obi Wan that the republic is in Sith control?