As far as I recall, rebuilding Shep and constructing the SR-2 are about the only two Cerberus projects that had any significant benefit without some ridiculous terrible cost.
They're responsible for the birth of Human Biotics, caused by them deliberately crashing ships and spilling Eezo everywhere, which of course resulted in hundreds of birth defects and stillbirths.
There's Project Overlord, which I would actually find forgivable given the intentions and the relatively small cost of one life, except a) it yielded no results and

went wrong like virtually everything else they touch.
Rachni, went wrong, people died, Thorian Creepers, went wrong, people died.
Christ knows what they were even trying to do with Akuze.
Not to mention every single thing they did in ME3. Indoctrinated or not, it was their own fault for being catastrophically stupid with the Collector Base.
Ultimately, I actually find some of their methods forgivable. And yes, in some cases I think the terrible things they do could be justified by the results, Overlord for instance. But more than once they've gone too far for too little gain. Their propensity for failure certainly doesn't help their image either. Sometimes they're like a bunch of idiots who think they can get their way by throwing money and dead bodies at a problem, which is made even worse by the fact that they often fail to solve the problem itself.
That said, I think the contributions they have made should be acknowledged. Even so, their only goal has been human dominance, despite what some may say. I don't have anything against a pro-human group, but Cerberus isn't just about bettering humanity, but about claiming a largely undeserved position at the top. So whilst some humans might be able to say that in their favour, about 90% of the galaxy has no reason to even attempt to forgive anything Cerberus has ever done.
Short version - if they weren't such a f*** up, maybe they could be vindicated, but they've pulled too many stupid antics for that at this point.