Malik's death in Revelations was tragic and violent enough as it is, but if you take into account how Altaïr's relationship with Malik began, it feels very targeted on Abbas's end.
Think of how it began with Altaïr's worst mistakes, getting his younger brother killed and Malik's arm ripped off. I'm sure Abbas was there to see him nearly expelled from the brotherhood, I'm sure he heard the fate of the Al Sayf brothers. Only for Altaïr to take that horrible mistake and its consequences and become the best possible version of himself, from unable to handle any responsibility to becoming the youngest mentor the brotherhood ever had. Even his relationship with Malik would go from animosity to close and trusted friend. You could argue that Malik was his GREATEST friend, other than Maria and his own children. The kind of growth and maturity it would take from both of them to get to that point is frankly astounding and for all Ubisoft's faults I think AC1 and Revelations did their due diligence with that
And then Abbas took that all away from him and never let Altaïr move past those mistakes he worked so hard to correct. How do you think he felt, being sent the severed head of the man started his journey with by severing one of his limbs? The mistakes of his youth cost Malik his arm, and now they've cost him his life in such a way that defiled and violated his body even more horrifically, after Malik trusted and loved him like a brother.
I like to think that Malik died protecting Sef from wrongful execution and defending Altaïr's honour. That the man who faced some of the bloodiest consequences of his past mistakes kept his youngest son safe and his reputation intact at the end, even at the threat of death for himself.
Hell, I imagine Malik was a bit of an uncle figure for Darim and Sef growing up. Perhaps the very thing that got him executed in the end was trying to keep Abbas's blades away from Sef.