Because the whole potential situation is mortals using their Free Will to make decisions.
Free Will is a bitter sweet gift, and this are the downsides of it, humans can be wrong. If Merlin made the Free Will decision to execute Molly TWG wouldn't intervene the same, as he wouldn't stop Michael from drawing the Sword and attacking the Council for it. But the Sword wouldn't have any power besides being a sword since he doesn't use it with a) clean intentions (vengeance) b) in the way the Sword are supposed to be used (in protection of mortal Free WIll)
This whole situation simply doesn't fall under the purview of things where TWG and Angel intervene. The precedence where they do are clear and established, infringement on mortal Free Will by supernatural powers, or supernatural powers going against their intended purpose.
Yes TWG stacked the chances in Mollies favour (Dresden's belief, the arrival of the rest of the SC saved by Michael) but in the end, this is all he can do. In the end, it is mortal will against mortal will. TWG, Angels, and the Swords have nothing to do in this conflict.