Humans have the ability to be murderous and cruel. We also have the choice to not be murderous and cruel. Cylons also seem to have the ability to make that choice, it is not a choice that has presented to them to make.
Sharon didn't just violate her code once. She did it a number of times.
Please read this article and this article. In particulare, compare the example that Dr. Hare gives that he suggested for the movie Malice with the scene between Capria 6 and the baby in the miniseries. The problem is that almost all of the evidence in the show is that the Cylons are all psychopaths without a conscience.
What gives a human "humanity" and makes them truly trustworthy is a conscience. A human without a conscience can never really be trusted, because they lack the conscience and empathy that make normal humans consider the impact of their behavior on other. All of the evidence so far, from Caprica 6 and the baby through the occupation of New Caprica and treatment of Baltar by Caprica 6 suggest that the Cylons lack any real conscience or empathy. It's all about them.
What about Sharon? A lot of her behavior is self-centered and about what she needs. When her needs change, so does her behavior. Do you expect her to remain a good soldier if she finds out that the baby was alive and she was lied to? I don't. She's a bomb waiting to blow up, just as she was before she shot Adama. Let's not forget that she's changed her mood and mind over and over again, as the situation changes. What makes you sure tht this is the real Sharon and not just act?
But let's assume that Sharon and the Caprica that loves Baltar have some small measure of empathy and conscience. Hare and others estimate that up to 4% of all people are psychopaths, with only a fraction of those becomming serial killers and so forth. The rest become those people who use and abuse others for fun and profit and just can't be trusted. Let's flip that percentage around. Let's suppose that 4% of Cylons actually have a conscience. Can humans really put their entire future and the survival of their species at risk in the hope that either the psychopaths will leave them alone or the 4% will be able to control the other 96%? Where do you think things would have cone on New Caprica if the people hadn't left, given that the executions were starting?
In short, I think you are projecting human assumptions onto machines that aren't human (and to the credit of the writers, don't think or act quite like normal humans). Consider this quote, from the second article, "Since everyone simply assumes that conscience is universal among human beings, hiding the fact that you are conscience-free is nearly effortless." Don't assume the Cylons have a conscience because nearly everything we've seen so far suggests that they don't.