I don't recall facing the issue like yours when org gets auto-installed as
dependency. But I found it annoying to wait for org to get installed as
dependency magically when some package having that as dependency got
updated. So I would delete it manually, some package would get updated, and
it would get installed again.

So eventually I came up with this and this has worked fine:

;; http://emacs.stackexchange.com/a/26513/115
(defun modi/package-dependency-check-ignore (orig-ret)
  "Remove the `black listed packages' from ORIG-RET.
Packages listed in the let-bound `pkg-black-list' will not be auto-installed
even if they are found as dependencies.
It is known that this advice is not effective when installed packages
asynchronously using `paradox'. Below is effective on synchronous
package installations."
  (let ((pkg-black-list '(org))
        new-ret
        pkg-name)
    (dolist (pkg-struct orig-ret)
      (setq pkg-name (package-desc-name pkg-struct))
      (if (member pkg-name pkg-black-list)
          (message (concat "Package `%s' will not be installed. "
                           "See `modi/package-dependency-check-ignore'.")
                   pkg-name)
        ;; (message "Package to be installed: %s" pkg-name)
        (push pkg-struct new-ret)))
    new-ret))
(advice-add 'package-compute-transaction :filter-return
#'modi/package-dependency-check-ignore)

On Tue, Jan 24, 2017, 3:55 AM Alan Schmitt <alan.schmitt@polytechnique.org>
wrote:

> Hello,
>
> I recently had one of those transient problems that go away when
> reinstalling org (the one where no code block can be executed). As I was
> doing so, I noticed that I had both org and org-plus-contrib installed,
> visibly because some packages depend on org.
>
> Is this a bad thing? And is there a way to make sure package
> dependencies pick up org-plus-contrib when it is installed, and do not
> install org as well?
>
> Thanks,
>
> Alan
>
> --
> OpenPGP Key ID : 040D0A3B4ED2E5C7
> Monthly Athmospheric CO₂, Mauna Loa Obs. 2016-12: 404.48, 2015-12: 401.85
>
-- 

Kaushal Modi