Bane was a constant reminder to Ra's of the hellish torment and death that his wife suffered in the prison. Ra's was also uncomfortable about Bane's love for, and protective nature around, Talia.
For those reasons, Ra's himself had Bane excommunicated.
Source provided by Ben Osborne, The Dark Knight Rises script.
[Ra's Al Ghul] saw only a monster who could
never be tamed. Whose very
existence was a reminder of the
hell he'd left his wife to die in.
He excommunicated Bane from the
League of Shadows. [Bane's] only crime
was that he loved me. I could not
truly forgive my father...
Until [Batman] murdered him.