When you disable a commission rule, you are turning it off for any future commission calculations without removing any of the existing commission records. Disabling a commission rule does not change the status of any commission records related to the rule.
If you would like to remove the rule and any commission records associated to it, you can select 'remove' on the rule. If you remove a rule with commission records, the commission records are also removed.
If you want to remove the rule but not loose the commission records, you should 'disable' the rule. Disabled rules are not visible to sales agents when logged in.