The critical difference is that you are intending to treat an illness; the death of the child is an undesired but unavoidable side effect.
Contrast this with an abortion procedure, where the object and intent of the procedure is to kill the child and remove her body from the womb, usually in bits and pieces.
And I am a Catholic who would never want to be involved in an abortion for any reason. I would feel tremendous guilt for the rest of my life, even if the abortion was done to save the mother.
It sounds to me like your conscience doesn't really believe that it is "excusable", then. People don't feel "tremendous guilt" over something that they truly believe is "excusable".
A better argument is this.
No treatment, child and mother die from ectopic pregnancy.
With treatment, you can save the life of the mother.
not true-—if a loved one was in mortal danger due to a pregnancy, I might support them in the decision (depending on the circumstances)-—but I would be very, very torn about it. I would have issues with it for a long time afterward.
I would have serious issues if I killed someone in war or if I was a police officer or if I had to for some other reason, even if I was protecting myself and others. The death of a human being for any reason is a very sad thing, because life is a precious gift from God and we shouldn’t be cavalier about it for any reason.