No SD, you are misspeaking. The Church condemns all procedures which directly take the life of the child, inlcuding the use of methotrexate and the direct removal of the embryo. The Church's concern is the morality of actions, not the consequences of the actions, because we believe that it is our actions and intentions by which we will be judged, not the outcome of the actions. Its the difference between being prosecuted for murder for accidentally shooting someone and the prosecutor stating it was obviously an accident and unitended.
You cannot licitly directly kill an unborn child to save the life of the mother, even if the only other possible result is that both die. Life is risky, and we should be prepared to move on when the risks go against us, not committing murder to extend it.
There is the additional consideration in the case of ectopic pregnancies that the embryo should be baptised if at all possible once removed with the pathological part of the fallopian tube.
What is getting you confused is that you are not considering the principal of double effect. Namely, if an action has two results, one good and one bad, the good result can justify the action if it is the intended and normal outcome of the action, even if the bad result shoudl also follow.
So, a woman may have her ovaries removed to cure ovarian cancer even though it is also a procedure of sterilization. Likewise, a ectopic pregnancy may be removed inside the fallopian tube even though the child will die. The bad result is a consequence of the good (curative) medical action, not the intended result.
The way you are looking at it, the good result, the cure of the woman's ectopic pregnancy, is the end of a bad action, the murder of an unborn child. That is obviously wrong. The end (cure of the woman) does not justify the means (murder of the child).
Don't we have a right to self-defense? Including the taking of another's life who is a direct threat? (Obviously if less-than-lethal methods are available, we would choose them.)
SD