During a second surgery, Alejandro killed his brother. Alejandro's girlfriend is pregnant and they are having a daughter. Alejandro killed Silvio because he could not risk the safety of his daughter in the future. He knew his brother was sick and as he said, Silvio had shamed their family for the last time.
He left the operating room with Escobar Gallardo and it is assumed that he was still working for him.
Following Escobar's facial reconstructive surgery in season 4, Escobar kills Alejandro in Sean's house as an act of goodwill, giving Sean the remaining "evidence" of Silvio's death in season 1.