Melisandre probably would have burned a child but there were motives involved and that course of action may have benefitted mankind regardless of her opinion on the doing the "greater good". If Melisandre's so called "greater good" was her teaching people not to mess with her by burning one of their own, then that's not exactly the greater good.
Now if Melisandre took some level of pleasure or burned people at will then yes she would be cruel. If she decided to burn at random or decided to burn someone's child out of spite, then that would be cruel. Melisandre simply does these things when it's beneficial to her cause, she's not doing it maliciously. Does that excuse her actions or mean she isn't bad? Absolutely not, but she is not cruel.
At some point though, you have to draw the line when it comes to a motive excusing a despicable act. And not everyone draws the "greater good" distinction in the same way that others do. Melisandre's "greater good" is someone else's "batshit crazy over a diety that doesn't really exist."
ETA: And there is no way in hell that Jon sent Gilly away with Mance's baby believing that Gilly's real son would be burned. The point was to send the "royal" baby away and, in all likelihood, own up to that fact if Stannis and/or Mel got it into their heads to hurt Gilly's son. The idea that Jon chose one child over another or actually thought Gilly's baby would be burned or would have allowed Gilly's baby to be burned is so out of left field it's almost not even worth addressing. He might have laid it on thick for Gilly to get her to, you know, give up the baby, but absolutely nothing suggests that Jon would have allowed either child to be burned.
Edited by Apple Martini, 29 January 2013 - 08:02 PM.