Rhaenys was ready to burn them all. However, Alicent standing in front her children moved her. She is/was also a mother.
They don’t deserve to die because the Greens followed Westerosi male primogeniture rules and installed Aegon on the throne. They also operate under the belief that Viserys would have preferred this on his final day, regardless of whether or not they believe it.
Rhaenyra should ultimately decide what to do about the Greens.
She also doesn’t wish to be remembered or cursed as an ancestor.