Shepard isn't any worse than Saren or Vasir, it's really how you perceive their motivations.
Like Vasir mentioned, working with Cerberus is probably worse than working with the Shadow Broker. The Broker may fund projects that keep the galaxy in shape, but he doesn't act as the engineer or boss of the project. TIM on the other hand, he has a personally say on the cells under he's command (though some tend to go rogue just to satisfy him).
If I had to pick a lesser evil, it would be the Shadow Broker, plus, he sells information on a plethora of things...not every intel he contains lead to a certain doom, just look at Vasir, she used he's knowledge of the current events to save lives many times over. Same can be said for Cerberus, they're advancing humanity in the most extreme way, for the better or worse.
Hell, even Saren wanted to protect the galaxy during ME, but Sovereign got the better of him. Shepard is fighting for the same cause as Saren, to save the galaxy. The only difference between their motives was how they operated. I'm not getting into details, the point is that there will probably be no Spectres that didn't have to coperate with the dark side <.< , the council knows this, thats why they're granted immunity from citadel law(well that what I think anyhow).
I'm not saying that Shepard, Saren or Vasir are the lesser evil, it's how people perceive them that makes them look so. Calling Shepard a good spectre would mean that Saren and Vasir are good as well, they just chose a different path towards their goal.