How to disable Commerce, but still have the module for later use?
Drupal modules in general can be disabled and uninstalled without major problems. Last version of Drupal Commerce (1.5) includes 20 modules, and some of them are totally independent. You definitely can disable Cart and Cart UI modules without disabling others such as the Product and Tax modules.

However, there is an important bug in Drupal Commerce relevant to re-enabling modules that it's still not fixed. See http://drupal.org/node/1361562