Shalom and thanks for your question.

There are two types of cases. In the case of a father stealing from his son, we know that the father will have mercy on the son, thus the son may not kill him. In any other case we are sure that the intruder is a potential murderer, thus the victim may kill him.

In our Gemara, Rashi is referring to an intruder other than the father. In Shemos Rashi is dealing with a case where the father is the intruder.

All the best,

Yehuda Landy