First of all, I just realized that I actually didn't answer your question in the last reply, so will just do that here first:
https://undsci.berkeley.edu/article/0_0_0/whatisscience_12
You are correct that science doesn't answer moral questions, for instance we can use science to create an atom bomb which we can use to blow each other up, but science doesn't have a stance on whether that is morally right or wrong.
There are limitation whenever we have a lack of evidence, which means that the critical thought process will be less reliable and we might have to make use of less certain ideas or experiences to help make us make a decision.
So for instance, lets imagine a hostage situation and the negotiator is working with an unstable person, the negotiator have very limited knowledge about this person, but might have former experience from dealing with similar situations which might be useful or it might not. So the negotiator will be able to use critical thinking only with limited effect trying to figure out which approach might end in the best possible result.
But in cases where evidence is present, making use of critical thinking is highly useful. For instance, lets say that you are given the option to walk over a metal plate and can see fire underneath it, which you know will make it burn you. Clearly using the evidence or knowledge of fire and metal, will make you choose not to do it.
So using your wife as example, to the best of my knowledge, she will also use critical thinking to determine which approach is best in a given situation, should she lean on the religious stuff? or is it better with the other approach. But critical thinking about this as also stated above, doesn't say anything about whether this is moral right decision or not.
But we can use critical thinking when it comes to morality to judge and examine each others arguments. For instance, a person might argue that people of a specific skin color is worse humans than others are. But by using critical thinking, we can evaluate their argument. Which is also why I said that critical thinking might in fact be necessary in order to do moral evaluations in the first place, because it gives us a method or approach to do this.