Interesting about the ugly / beautiful thing.
If we consider as a group those characters noted for their physical beauty we have:
Cersei - cunning, ruthless, vindictive, self-interested, ambitious
Sansa - initially shallow and naive, but basically honourable and decent
Margaery - manipulative, ambitious, but as yet has not done anything very deplorable
Daenerys - has many admirable qualities, some small flaws but overwhelmingly "good"
Jaime - initially as Cersei, now undergoing a sea change
Loras Tyrell - largely unknown, no overtly despicable acts as yet
Rhaegar Targaryen - again not much is known, but does not seem to have been an evil bloke (cannot say much as this is a spoiler-free thread)
Joffrey (notably attractive in books) - evil, psychotic, no redeeming features
Melisandre - ruthless, but motives as yet unknown
So quite a mixed bag.
And those characters noted for their physical ugliness or deformity:
Tyrion - likeable, honourable, decent
The Hound - initially a thug, committed deplorable acts; was not sadistic; bitter, jaded and nihilistic; also showed sporadic signs of compassion, pity and kindness; possibly on some sort of redemptive path
Brienne of Tarth - extremely good, decent and honourable
So I am not sure that GRRM is saying anything in particular about a link, inverse or otherwise, between physical beauty and moral goodness
unless it is simply that (to be trite) you can't judge a book by its cover 