Rav Shimon writes [כתובות סי' ד עיי"ש] that when there is a היתר to kill it is not considered a מעשה רציחה. So killing a בא במחתרת isn't רציחה.
Chazon Ish: The Gemara [Yoma 85b] says:
ענה ר' ישמעאל ואמר (שמות כב, א) אם במחתרת ימצא הגנב ומה זה שספק על ממון בא ספק על נפשות בא ושפיכות דמים מטמא את הארץ וגורם לשכינה שתסתלק מישראל ניתן להצילו בנפשו ק"ו לפקוח נפש שדוחה את השבת
Rabbi Yishmael answered and said that it is stated: “If a thief be found breaking in and be struck so that he dies, there shall be no blood-guiltiness for him” (Exodus 22:1). Now, if this is true for the thief, where there is uncertainty whether he comes to take money or to take lives, and it is known that bloodshed renders the land impure, since it is stated about a murderer: “And you shall not defile the land” (Numbers 35:34), and it causes the Divine Presence to depart from the Jewish people, as the verse continues: “In the midst of which I dwell, for I the Lord dwell in the midst of the children of Israel” (Numbers 35:34), and even so the home owner is permitted to save himself at the cost of the thief’s life, then a fortiori saving a life overrides Shabbat.
You see clearly from this Gemara that בא במחתרת is רציחה??!!! As the Gemara says "ושפיכת דמים מטמא את הארץ"!!!
