I thought the guy who killed sef blamed it on Malik (MASSIVE SPOILERS) and locked him him up Altair saved him and nursed him back to health but sadly the guy who killed sef sneaked in a decapitated Malik he then showed it to both Altair and Maria (NOT Ezio's mother)
I know it's not Ezio's mom lol and well it has been forever since I last played but according to my research it says (SPOILERS!!!) that Abbas told his apprentice/spy, Swami to stab Sef to death so that he could take control of the Order for himself. In the moments just before killing him, Swami told Sef that it was his father Altair who ordered the execution.
(SPOILERS!!!) After killing Sef the murder weapon was placed in Malik's bed and had on elf his spies say that he had overheard Sef and Malik arguing over who would regain control when Altair returned. Long story short Malik was framed for Sef's death and thrown into prison in the dungeon's beneath Masyaf.