I don't think that Snape's soul was damaged to an extent that the good in him was gone. He was operating under the instructions of Dumbledore, for the good side, working against Voldemort. As a show of faith to the dark lord, he may have had to do things he would otherwise not have done. But for his initial crimes, he was filled with remorse for first, having pointed out the Potter family, and second, the deaths of Harry's parents..especially that of Lily's.

Regarding Draco, I think Dumbledore didn't wish to tarnish a soul that was still untouched. Once a crime has been commited, you are a criminal until you've paid your debt. And what Draco was about to commit was cold blooded, calculated murder. And just because a soul can heal, it doesn't mean it won't bear the scars of its past. Every wound leaves a mark.

Correct me if I'm wrong, but is JKR trying to suggest through Dumbledore that mercy killing is okay? Or is this not a message and just the veiws of a dying old man who seems to think that it is okay to kill someone if the victim gives you permission first?

I can find only one angle to work this. JKR might have meant that neither Dumbledore nor Harry could help Voldemort now if he did not wish to help himself. You can't make a person feel remorse if they have no desire to. Or maybe he was too far gone down the path he chose and was beyond any help.

I think Harry is just making Voldemort aware of his wretched situation here.