As a rule superheroes don't kill unless it's absolutely necessary, and writers have been using this moral dilemma to their advantage from the very beginning.
In fact, so many story arcs would have ended before they even began if superheroes would just kill the bad guys and get it over with, but heroes are more likely to kill one of their own than their wicked foes.
Wolverine is often seen as a savage fellow and therefore has no problem killing his foes, but one kill definitely weighs heavy on his conscience- the time he had to kill Jean Grey.
Jean Grey was resurrected by the Phoenix Force hoping to become Dark Phoenix once again, but this time Jean was prepared to fight the Phoenix- with a little help from Wolverine.
Logan was forced to kill the woman he loved over and over again, weakening the Phoenix Force so Jean could separate herself from it, and all he knew was murdering Jean Grey was the only way to save her from that cosmic force.
Wolverine isn't the only superhero who has killed a loved one- Namor the Sub-Mariner was also forced to kill his lady love for the greater good.
But Wolverine isn't the only hero who had to kill the love of his life for the greater good- Prince Namor the Sub-Mariner
It seems his beloved Marrina's alien DNA had a very strange reaction when she became pregnant with Namor's child- the pregnancy transformed her into a gigantic sea creature.
Namor was forced to do the "right" thing by using the Black Knight's Ebony Blade to slay Marrina, which may have contributed to Namor's anti-hero conversion.