I think that Sandel's writing overall is much less aggressive than Harris'. I definitely don't feel that I need to defend my right to my own reasoning as much. I also feel that he isn't coming down so hard at one end of the spectrum. He's more arguing for caution in out pursuit of science and laying out the ways such technology could effect us physically and socially. Which I think would be best.
He also fills in the (probably intentionally) omitted rest of Habermas' point on autonomy. I suspected there was more to his argument and my skepticism of Harris' fairness and depth of understanding turned out to be valid. Habermas makes his point on the reduction of autonomy, and then adds an important caveat: It is something different when those things out of your control are determined by something out of everyone's control. That is to say, It is different when nature or God makes you the way you are than when another person has decided it for you. Though Harris would balk at this assertion, I think it is a valid observation. Intent is very important to human morality; we have two different criminal names for the same result: manslaughter and murder. Anyone could probably forgive someone who killed someone they love on accident, but it would take quite a person to forgive someone who killed a loved one intentionally even though they loose someone either way. If we are arguing pure morality, Intent should have a big effect on our discussion.