General Coding Guidelines, paragraph 4 & 5:
Code or codes from 001.0 through V91.99 must be used to identify diagnoses, symptoms, conditions, problems, complaints or other reason(s) for the encounter visit.
The selection of codes 001.0 through 999.9 will frequently be used to describe the reason for the admission/encounter. These codes are from the section of ICD-9-CM for the classification of diseases and injuries (e.g., infectious and parasitic diseases; neoplasms; symptoms, signs, and ill-defined conditions, etc).
That is taken straight from 2014 ICD-9-CM which tells me that any diagnosis active during the "hospital admission" can be used throughout that admission to describe E/M visits and procedures. So, 458.9 is not an unacceptable or inaccurate diagnosis code for removing the IABP. The patient's condition is illustrated through CPT and ICD-9 codes, not just ICD-9 codes. The payer already knows the device is being removed because that is the exact definition of 33968. Typically, the claim for the removal is sent a couple days after the claim for the insertion 33967, so the payer is already expecting to receive a charge for removal. V53.39 isn't necessary and is too generic for this situation.
Also, what about coding for MI or a chronic condition? If a patient is admitted to the hospital for an acute MI of the anterior wall the appropriate diagnosis code is 410.11, right? Immediately intervention is performed which resolves the acute MI. Subsequent visits for that patient during that hospital admission will still be coded with 410.11 along with all other relevant ICD-9 codes because that code demonstrates the reason for the visit. Same goes for chronic conditions like atrial fibrillation. Sometimes a patient will have atrial fibrillation for years but occasionally will spontaneously convert to normal sinus rhythm. Even when the patient is not in atrial fibrillation we would still code an office visit with 427.31 because it is an ongoing chronic condition and it will be taken into account when changing medications or ordering diagnostic tests.