After rereading the Pensieve scene of the sentencing, I have to say that I really think she knew he was guilty. They had already had the trial and this was only the sentencing. Crouch, Sr. states that they had already heard the evidence against them and they had been found guilty. The way Mrs. Crouch reacts just doesn't strike me as someone who believes an injustice is being done to her child. If she believed he had been falsely convicted, I think she would have been very angry with her husband. At the very least, the fact that she is there, sitting beside her husband who is the one passing down the sentence on their child, indicates to me that she knows Barty Jr is guilty. Otherwise, I think she would have rejected everything about the sentencing, including her husband. But sitting there, rocking back and forth whimpering is more the behavior of someone who realizes the situation is hopeless. I really think she knew he was guilty.
That being said, even if I did think she thought he was innocent, I don't know if I would change my opinion on her Slytherin traits. I might lean a little more towards Gryffindor, because then things would be a little more on the chivalrous side, (defending the innocent), but I would still see the Slytherin in her, too. Her actions were still more devious and calculating than bold and daring. I just see a Gryffindor standing up and shouting out their belief in the innocence, sort of "Don't worry, Son, I'll save you. I'll prove you are innocent!" rather than sitting by while he was dragged off and then sneaking in and breaking him out only to have him hidden away, imprisoned in their own home all those years.
So my money is still on her being a Slytherin.
You know, I think the Crouch side story is one of the saddest, most heartbreaking parts of the series.