I can totally see how this story will work: by acknowledging said elephant.
My way-too-early prediction is that we will see a new Clark Kent in the pilot episode who will introduce the audience to Kara and basically set things up. Clark (whom we'll probably never really see in costume) will explain that it's time for Kara to leave the nest and start her own life and that he'll be around if she needs him (but most times she won't). Clark may show up maybe once a season, always in civilian gear, and only when he's in town to visit (and he can never stay long: Metropolis or Lois or the League or the world in general constantly needs his attention elsewhere) and offer support and advice to Kara in a non-overbearing big brother fashion.
I'm hoping Kara picks the Karen Starr identity and this show's theme becomes the Journey to Power Gal (deliberately misspelled).
Also, www.ign.com has a way-too-early but interesting article on who should play Kara on CBS's SUPERGIRL:
http://www.ign.com/articles/2014/09/...play-supergirl
Out of their 7 choices, two of them stand out: Leven Rambin (SARAH CONNOR CHRONICLES) and Britt Robertson (UNDER THE DOME) look the most like what I think of Supergirl.