I think that there is some confusion here about what exactly constitutes a soul. Echo has developed access to all of the PERSONALITIES that she has been programmed with over the time of her stay in the Dollhouse, and, in fact, the personality of Echo, and even Caroline, are merely personalities. The soul is something much more than a mere personality, though it would take someone far more eloquent than I even pretend to be to properly explain the difference. Joss uses the concepts of soul and conscience pretty much interchangeably, and that's not a bad comparison for our purposes here. We've never actually seen Echo/Caroline, regardless of what personality that she has been programmed with, do anything evil or cruel (there was that one time with the leather outfit and the whip, but that was kinky, not necessarily cruel), so we really can't judge whether or not her conscience would allow whatever personality she was currently using to do it. Personally, I doubt it. As far as we know, the only really evil, cruel doll was Alpha, and he might very well have been cruel and evil to begin with.
In answer to the original question, though, I guess that it's basically a matter of personal opinion, and my opinion is that the soul is something beyond personality, something that is constant and unalterable. It might become tarnished, but it always remains basically the same, regardless of any outside factor.