It’s not unprecedented that a monarch might execute the head of a noble house and make peace with the heir of that house. Considering that the heir is likely the child or close relative of the previous head of the household, the forgiveness is significant. Familial guilt is somewhat foreign to modern, western sensibilities, but looms large in many historical and some modern cultures. The fact that all of the descendants and relatives of the guilty party are not considered to bear that guilt is meaningful forgiveness in this context. Even for the executed person, it allows for the ability to leave a legacy that can carry on the name and influence and could constitute a real negotiating point in a peace deal.
That said, I think that the question is more the degree to which this was a betrayal of trust on Morgase’s part. Did the heads of households negotiate a deal that they understood would mean their own deaths because it would allow their families to survive? Or were they lead to believe that they would be allowed to live and then deceived?