With regard to the torture of the prisoner. The prisoner had aided and abetted in a genocide. Let us not forget this. Above all Cain wanted information. One of the ways she wanted to accomplish this was by psychological torture and degradation. Torture has been used by both "good guys" and "bad guys" throughout history. Watch Zero Dark Thirty.
With regard to raiding the civilian ships...in a lot of wars throughout history including WWI and the Civil War (the good guys...the Union did this), there was a common tactic utilized called scorched Earth where an army would destroy anything - food, homes, etc. that could be considered useful to the enemy. Lots of civilians died as a result of these tactics. At least Cain was just scavenging for things she needed. Judge her not to harshly.
I think the end of the Pegasus arc and Razor pretty much vindicates her. At her funeral Starbuck says the fleet is less safe without her and everyone on Pegasus pretty much agrees with this. Towards the end of Razor Adama acknowledges that he can't find anything wrong tactically with anything Cain did and refuses to render a moral judgement on her. And I think what symbolically vindicates her is that her protege Kendra Shaw is promoted to XO in Razor and sacrifices herself in battle at the end. Adama recommends posthumous commendation for Shaw despite the self-righteous objections of Lee. Adama also tells a shaken Lee that his decision to sacrifice Starbuck, Shaw and the away-team (overruled by Adama) wouldn't have been the wrong decision implying Cain would have made that decision in a heartbeat.