How to programmatically remove a user from an organic group
Part of me thinks that og_membership_delete would be a good option, you can pass the entity ID in as a parameter (and by "can", I really mean "need to"). Also, og_ungroup seems useful as well. 

You can find more functions that OG defines at: http://www.drupalcontrib.org/api/drupal/contributions!og!og.module/7

Here's an example of og_ungroup:

og_ungroup('node', $gid, 'user', $uid);