I think YED was pushing right up to the absolute edge of the rules when he bled into the kids with their parents rather than their own consent.
It's like the situation in Reaper, where Sam's parents sold his soul to the Devil. And Sam's friend Ben points out, quite rightly in my opinion, that they couldn't -- that a soul can only be given up by the person to whom it belongs. Sam would have to make that deal, not his parents.
So SPN Sam, and the other psychic kids, were tainted by demon blood through no volition of their own. Their parents made them the sacrifice. So sure, burn Mary or the other parents, but it's Just. Not. Fair. to blame the kids for something that was done to them when they were 6 months old. Of course, in the SPN-verse, as in the Bible, things are seldom fair.
Also, I'd accept the argument that while the source of the power is negative, the kids can't be held liable for anything until they actually do something evil with it. (Like Andy -- was he doing bad, or was he just annoying and amusing? And Eva was trying to be helpful by warning Sam about the visions. It wasn't until the YED got to her that she turned evil. As far as we know Jake didn't do anything bad with his superstrength - he saved someone's life, that's all we know - until the YED arrived. Lily is more problemmatical. But she didn't electrocute people deliberately.) So Sam has powers that may come from a dark place. But he resisted the YED's efforts to make him turn to the Dark Side of the Force.
The question is, is what Sam's doing now evil? Or enough to put him at risk of turning evil? And if so why, because I honestly still don't see it. (To recap: exorcising demons, good. Leaving hosts alive, good. The angels don't like the methods? I don't suppose they'd enjoy the irony of turning evil against itself.)