After some thinking and research, the answer turned out to be trivial: git rebase -i takes the editor name from the well-known EDITOR/VISUAL environment variables, so overriding that to point to a non-interactive script does the job.
However, EDITOR/VISUAL applies indifferently to the list of commits, commit messages when rewording and anything else. So, since http://git.kernel.org/?p=git/git.git;a=commit;h=821881d88d3012a64a52ece9a8c2571ca00c35cd , there’s a special environment variable GIT_SEQUENCE_EDITOR which applies only to the commit list.
So, the recipe to re-order or flatten commits is:
Run: GIT_SEQUENCE_EDITOR=<script> git rebase -i <params>.
Your <script> should accept a single argument: the path to the file containing the standard rebase commit list. It should rewrite it in-place and exit. Usual rebase processing happens after that.