It helps to make the enemies distinctively evil or non-human, like evil minions, monsters, robots, etc. That way the violence feels a little more..justified?
Or you can make combat more comical - have enemies fly off the screen instead of exploding or disappearing, use stars or something instead of blood, etc. (In Metroid: Fusion, very few enemies actually die - instead they turn into X parasites and possess other enemies or just fly away)
One other trick that helps with this is enemy re-spawning like in Megaman X or something - nothing actually DIES, just returns to its original position with full health and such. This prevents the level from becoming desolate after killing everything, which could inadvertently make your game seem much darker.