Bitbucket asks the question about whether to close the branch in a pull request at the time you create it, e.g.,

  https://s3.amazonaws.com/uploads.hipchat.com/10804/29957/csa3g3hjsk6i27p/close-branch-after-merge.png

since the person creating it is usually in the best position to decide whether the feature branch they're working on is "complete".

Though I really like GitHub's implementation for cleaning up old pull requests (or ones you forgot to tick the close branch checkbox for).

(Full disclosure: I'm a developer on Bitbucket for Atlassian.)