Killing Magneto could have permanently Stagnated the effect of the earth's Magnetic state, increasing its decay, and As keen as Logan is to eliminate his foes, He's not heartless, Magnus wasn't wrong for being enraged or wanting revenge, but some unfortunate few become beholden to that Mission, so much so that death is really there only Release, also Logan caught Magnus off guard, he was never gonna be able to get another hit off after that
and i nearly forgot the man was a Samurai, (kinda sorta) the man still has Honor,