The question needs to be asked why the football club didn't charter a longer range aircraft to fly them directly from Chapeco airport (which has a 2475m runway) to Medellin rather than flying commercial via Sao Paulo to Santa Cruz and then booking what should have been a two leg charter. That would be 4 sectors in total which probably isn't ideal preparation for a cup final. It wasn't that the charter was cheap. From what's been published it would appear that the price of the charter was way in excess of what would be reasonable presumably due to various backhanders from the airline to officials in the football world.
It would appear that either the club were in on the scam or the Brazilian FA or CONMEBOL instructed them to use LaMia however inconvenient it was.