Hostages are only valuable if your opponent knows you're willing to kill them, and a big part of the whole system is tit for tat. If two sides have hostages, and one side kills a really important one then the other side has to respond by killing someone or several someones to even the scales. Not doing so tells the other side they can kill as many hostages as they want without repercussions.
There's also the fact that the Northern lords will pretty much demand it of Robb - canon Robb didn't have someone equal to Ned's worth as hostage, but here we've got Tywin.
Jaime's worth was not equal to Ned's, and he was the only real hostage of significant value they had in their possession. Killing him would have forfeited Sansa's life (and Arya's as far as they knew), so the restraint was at least understandable in that case. The situations aren't equal. Killing Tywin still leaves us Jaime, Tyrion, and two of Kevan's sons (with no angry Karstarks wanting to murder them, as far as we're aware, and Kevan's importance increased due to Tywin being captured).