In other words, Logan's popular, so it's okay when Logan does it. Gotta be on the right side.
Wolverine has been killing people in the comics for decades, its an expected part of his character. Outside of Elseworlds stories and a few terrible mistakes (like byrne's horrible junk), Superman isn't a killer. Him not killing is usually a big part of his character. So, yeah, it is ok when Logan kills, but not when Superman does it. Same with, say, Punisher killing but not Batman (not counting golden age Batman who killed for a bit, but that never stuck to the character). A comic book hero or antihero killing being acceptable is very much decided on a case by case basis, based on who the character is.