It is indeed true that the Haiti earthquake disaster ranks among the highest ever loss of limbs for a single natural disaster, possibly the highest. However, since the Civil War was an ongoing war and as such not a single disaster, the comparison is both uneven and unfair.
While earthquakes happen all the time, the disproportionate amount of amputations in the particular Haiti disaster was due to many factors.
Construction codes are practically non-existent in Haiti, which is why buildings were made on the cheap. This is nothing new or unusual. And old Haitian joke was that you shouldn't fart inside your house -- or else it could fall over.
Unfortunately this was closer to the truth than thought. To save money most constructions lacked steel rods. Multistory buildings were built without or very little inner steel support, only with concrete blocks and cement. In addition to that cement was mixed with ocean sand, freely available. This saltwater-infused sand corroded whatever steel there was, making the walls extremely brittle.
When the quake struck, buildings that should have easily withstood the shocks, came crumbling down. As a result more buildings than should have fallen fell, trapping more people under the rubble than would otherwise have happened.
Life or Limb
Due to the unusual large number of victims with crush syndrome, rescue forces were unprepared. Most arrived with enough emergency tools and equipment, however lacked all of the necessary medical supplies and often time to properly treat crush syndrome.
Crush syndrome occurs when limbs are trapped for a prolonged time under heavy weights. This causes large quantities of phosphate, potassium, myoglobin, creatine kinase and urate to be released from the cells, which then leak into the circulation. This can then lead to ischaemic renal dysfunction which is deadly within a few days. The only option to counteract this is to treat the patient with intravenous sodium bicarbonate and attention in an intensive care unit.
But with literally thousands of victims coming in every few minutes, it was not possible to treat all individual crush cases properly to save the patients. The only other option was a quick amputation of the affected limbs. Field medics had to take triage decisions on the spot. Most of these required the removal of the crushed limbs. While it may have been possible to safe the limbs with proper care and treatment, there was no time or the resources to do so. Mass graves were dug for the limbs alone.
Therefor the Haiti earthquake became the natural disaster with the possibly largest amount of amputations in human history.