I'm not sure disabling validation rule is the only way out for this particular scenario but you guys can chime-in ideas how to approach this particular issue.
I have the following validation rules on my custom__c object
if(Attachment__c == FALSE && URL == null, true, false)
and a Trigger on before insert and after delete on the same custom__c object
........... ........... Attachment__c = false; update mycustomobject;
when I try to delete the row I'm getting this error:
execution of AfterDelete
caused by: System.DmlException: Update failed. First exception on row 0 with id xxxxx; first error: FIELD_CUSTOM_VALIDATION_EXCEPTION, Attachment is unchecked and URL is empty: 
I know exactly why I'm getting this error because its firing the validation-rule that i have place in but I'm not sure what is best practice to deal with this type of situation?