Do you play on a console, or the devil's machine (pc) ?
If it's the latter, consider downloading http://skyrim.nexusmods.com/mods/19. It fixes runes and their bad relation with the augmented perks, among a myriad of other bugs.
I'm on PS3.
Runes are not affected by augmented perks. this hasn't changed. that said, runes are still my favorite destruction spells. Until I get incinerate, I do most of my killings with fire runes.
Wall spells are affected by augmented perks. They do much more damage as traps and cost a lot less.
Too bad

. I love the rune spells for my character. It's so much fun to mess with enemies with quiet cast runes and throw voice. You can kill the hardest enemies with this without ever getting noticed.
But still more damage is always better :/.
I assume this tactic doesn't work with walls since the enemies will notice where the casting is coming from?