I have total respect for her as a character, but she works for a racist terrorist organisation - thus removing her as a possibility for an LI. Especially considering you can't romance her as a female Shepard anyway. That's also an important factor.
The Illusive Man chose the Normandy SR2 crew so that Shepard would try to think of Cerberus in a positive light. It was a form of propaganda. Even if each cell aren't aware of what the other cell are doing, there will be reports on the extranet detailing assassinations and the like and linking them to Cerberus, meaning that there is no doubt in the fact that they would know what type of organisation that they are working for. And while I see them being quiet about their operations, I can't see them being quiet about their opinions - much like the more racist organisations or political parties today. People will know what they are like. The members of Cerberus either agree with what happens, or choose to ignore it.
In terms of Miranda's resurrection of Shepard, she admits to wanting to adding a control chip in her mind. Those aren't the words of a noble woman. Those are the words of a woman who would consider the saviour of the Citadel as a pawn to push around in a way that she would see fit. She only thinks otherwise when the war effort against the Reapers hinges on Shepard's actions. Again, not noble, selfish.
As I said, I have total respect for the character. I think she's among the trilogy's best characters. But I disagree with the fact that you think she's noble. I think she cares about her sister, and sees Shepard almost as a necessity when it comes to ME3, but that's all. It may be different if you romance her though, or even for a male Shepard. But that's the feeling I got while playing a renegade femshep.