I've personally wondered about Cir-El myself. If they always intended to erase the character or not. Many theories fly around concerning her. Like DC made her purposelly just to erase so that we couldn't blame the new Kara's appearance for Linda Danvers removal.
I like to guess Loeb used her despite DC's insistence on getting ready to introduce nuKara.
Especially since Cir-El was in S/B #5 and new Kara debuted a whopping 4 issues later in #9.
I liked her alot and wished they would've expanded on her more.