I don't think there's a clear answer here, as the wording of the Charm hex is a bit ambiguous.
The text says that the witch improves the attitude of her target "as if the witch had successfully used the Diplomacy skill," but it's unclear as to whether this means Diplomacy was actually used (in which case using Diplomacy again would not work), or if the hex merely mimics the skill's effects (in which case I think it would stack).
Given that this ability has such a short duration, I don't see the harm in letting it stack with an actual use of Diplomacy, but ultimately I think it's up to the GM.