Her conversion to Catholicism was in the novel, not the film. Now, interestingly, some versions of home video for GFII open by showing Kay lighting candles in an apparently Catholic church, wearing a mantilla, as opening music plays. But that bit of film (very fine) never appeared in the theatrical release. So, it's questionable that Kay really did convert (in the films). And even if she did--to pray for Michael's soul--by the time of the "Tahoe Captivity" she was good and disillusioned (understated word)with Michael, and maybe with the Church, too.
As Apple said, a woman of her means could easily have paid a doctor to terminate her pregnancy at the estate--rich women could get abortions in those days. If there was a "nail in the coffin" at that point, it might have been in the coffin of Michael's regard for Tom, on whose "watch" the abortion occurred. Michael must have hated that Kay could "do this to him," the more so because it'd show that she was smart enough to figure out what he really was--and that all his BS about legitimacy wasn't fooling her.