Lord Zeuss wrote...
Their motivations and goals are not necessarily evil or malpurposed, and a lot of the actual people in Cerberus seem like very nice, well-intentioned people who would never dream of walking into an alien bar or an alien school with bombs strapped to their chest. The crew of Normandy SR-2 did not come across as fanatics at all, but rather honest people who were trying to do the right thing for their families, themselves, and even mankind.
In comes in the cell structure of Cerberus, and the Illusive Man. Cell structuring means that you can have one cell that is doing noble, commendable work to an honorable end, and another that is conducting horrific experiments on live subjects for some vague gain that is far outweighed by its horrendous cost. Neither cell knows of the other's existence, except for certain key individuals. Then there is the Illusive Man, who quite obviously lacks any sort of moral meter. He is not wrong for wanting to stop the Reapers, his problem is that often his means are not appreciably better than the Reapers.
I don't hate Cerberus as an entity, by this point they proven not only vital, but intrinsically needed. I was as honored to command SR-2 and its crew as I was the original Normandy. But I do not like, approve of, or condone the Illusive Man's at any cost mentality. Most people, when they say 'at any cost' still have a line they will not cross. The Illusive Man has no such line; he is driven entirely by the rigid lines of logic and algorithm. He is a human machine, lacking ethical judgment of any kind.
So I have no problem working with the Cerberus crew, and I'm sure as heck grateful for being brought back from the dead by Lazarus Cell. I like Miranda because she is capable of processing information on an ethical level, if rarely and selectively. The Illusive Man has demonstrated no such ability.
I think Cerberus is, as a whole, a deeply morally troubled organization to say the least, which has committed numerous crimes against humanity (Akuze, Jack, the husk experiments, etc.) and non-humans alike (their attack on the Flotilla in
Ascension). Not only that but they must have done something pretty nasty to get kicked out of the Alliance military black ops programs. I think Ashley's condemnation of them is wholly deserved.
That being said, most of the people you work with in ME2 from Cerberus aren't that bad. Miranda's an apologist and morally gray and I'd go so far as to say TIM is downright evil, but Jacob's a fairly well-meaning guy who seems to be aware of Cerberus' crimes but has, for better or worse, chosen to overlook them. Kelly, for her part, seems just plain naive.
I think what you said about TIM being able to do different things with different cells is largely true. The Lazarus Cell, in a way, is his PR cell. Sure, it's main purpose is to take down the Collectors but he assuredly has other cells working at that as well (such as the one tearing apart the derelict Reaper). But whereas people can look at Cerberus' actions in
Ascension or ME1 and easily condemn them, it becomes a lot harder to call Cerberus the bad guys when they have a bonafide war hero working for them, assembling a team of non-humans, and supported by very moderate Cerberus operatives like Miranda, Jacob, and Kelly.
Cerberus is still evil or at the very least
very morally gray at the end of the day. But they have you to put a good face on their works and, at the end of the game, you have a chance to possibly subvert TIM's plans.