I agree with this assessment, for the most part.
Ideally, Jones will turn out to be a man employing questionable means to a completely justified - and perhaps even objectively necessary - end. How does one stop a villain who's actually doing the right thing, or is doing something for the greater good? These villains are often the most intriguing ones to follow.
Though I agree that it's great when there is no clearly defined "bad guy"; it's only a bunch of people trying to do what they think is right and/or necessary, with these ideals often coming to a clash. I guess when we eventually hear Jones' side of the story, the field will be leveled to the nice shade of grey we so enjoy, and in turn place into new light Bell and ZFT, and what exactly they were trying to do.
This is in an ideal world, however; it can go in many different directions at this point, though I too dread the possibility of Jones being revealed as just another scientist with a God Complex.