For years, that moment has puzzled fans. "Killing is wrong, so I must kill you!" Even if you sort of kind of get where Wolverine's coming from, it's still a bit odd.
Well, reader Lance M. wrote in after reading the aforementioned CBR article and he asked if I knew that Chris Claremont years later gave Wolverine's "real" motivation for stabbing Rachel. I did not know that.
Anyhow, as it turns out, Claremont confirmed in a 1991 Comics Interview interview that Wolverine was afraid that killing Selene would trigger Rachel turning into Dark Phoenix, and thus he felt that he had to kill her to avoid the much worse fate of Rachel becoming Dark Phoenix. That honestly makes a lot of sense. It's not in the actual comic, but it DOES make a lot of sense.
Good to know! And now the rest of you know! Thanks for the suggestion, Lance!
EDITED TO ADD: Commenter Michael noted that Claremont had actually first given the "Dark Phoenix" explanation a year earlier in the 1990 Uncanny X-Men Annual, where Wolverine encountered Rachel for the first time since the stabbing (she was there with Franklin Richards from the future)...