Backing out of Drupal Commons
Nice question, but challenging. Basically you want to switch installation profiles (from commons to regular Drupal core). And that yielded some results on Google, including Profile switcher and This blog page. They might be of help during the process.

Before blindly installing modules, please read on, make sure you have proper backups (in fact try to verify your backup actually works) you might have to recover multiple times.
From what I understood these methods are usually from upgrading 'standard' Drupal to another profile, but it might work backwards.

I'd start by disabling and uninstalling (use the uninstall tab) all modules that come prepacked with your profile distribution. This will likely be the features, but there might be more. Then attempt the switch. See which method works best...