Dont get me wrong, Flora is a horrible person, but her actions towards Rune is not a prime example of her awfulness. She literally just gave her info and then forced her to not tell it to anyone. As for Huey, there's a decent chance that telling him about the reason for Rune's disappearance will make him aware of her connection to Bladestar, so even if she wanted to tell him, she probably couldn't. In your original post you compared the actions towards Rune and Huey to her irredeemable actions (Florin execution, Ryland, etc) ,which is what I tried to point out. I basically agree with the rest of your analysis. Also, Flora also took special effort in making sure her Ferrothorn wouldn't be hurt, so that's another moot point.
On an somewhat unreleated note, anyone has a video of Florin's execution? I tried to trigger it myself but I somehow failed.