The Torah does not view war the same way the Western world does. The Torah has it's own morality that is very different then 20th Western morality. Unfortunately, there are many Jews who are very affected by Western culture and have adopted Western morality over Torah morality. Below I outline the Torah's view on war. I am sure there will be many liberals and יפה נפש who will be horrified by this and call me a barbarian. However, this is what the Torah says. We need to follow the Torah's morality not Western morality.
I. כיבוש מלחמה
The Torah states that territory acquired through conquest is yours both for Jews and non-Jews. See the gemara in Gittin 38a. In other words territory that Israel conquered in 1967 is ours al pi torah based on the din of kibush milchama.
II. Innocent Civilians
The Torah does not recognize the concept of innocent civilians. The Rambam in Hilchos Melachim (6:5, 6:6) writes:
ואם לא השלימו, או שהשלימו ולא קיבלו שבע מצוות--עושין עימהם מלחמה, והורגין כל הזכרים הגדולים, ובוזזין כל ממונם וטפם; ואין הורגין אישה ולא קטן--שנאמר "והנשים והטף" (ראה דברים כ,יד; וראה דברים ב,לד), זה טף של זכרים.
ו,ו במה דברים אמורים, במלחמת הרשות, שהיא עם שאר האומות. אבל שבעה עממין ועמלק שלא השלימו, אין מניחין מהם נשמה: שנאמר "כן תעשה לכל הערים . . . רק, מערי העמים . . . לא תחייה, כל נשמה" (דברים כ,טו-טז), וכן הוא אומר בעמלק "תמחה את זכר עמלק" (דברים כה,יט).
If they do not make peace and do not accept he 7 mitzvos we make war and we kill all the adult males ...this is in a voluntary war but with the 7 nations and Amalek we kill everyone
We see that we kill all the adult males even if they are civilians.
III. Collective Punishment
The Maharal writes in Gur Aryeh (Parshas Vayishlach perek 34 pasuk 13)
Although the Torah reads ... you shall greet them peacefully, this speaks of a city that did not harm us. But as regards those who attack the Jews even if only one of their members was responsible for this act revenge may be exacted on the entire nation because he is one of them.
The Maharal writes explicitly that the Torah allows for collective punishment (this is how he explains how Shimon and Levi were allowed to kill the whole city of Shechem) if someon attacks you.
The Torah commands us to wipe out Amalek copmpletely men, women and children.
V. פיקוח נפש
There is no din of פיקוח נפש in war. The Minchas Chinuch mitzva 424 makes this point, otherwise the Jewish people could never go to war. The Netziv writes this as well (Kiddushin 45a) as well as the Brisker Rav on teh Haftara of Parshas Beshalach as well as other acharonim.
It is very clear that today the Palestinians are at war with the Jewish people as RHS states and as R' Yaakov Kamenetsky paskened and therefore we do not need to be ashamed at what has been done to the Palestinians, rather we need to say why are we risking Jewish lives to save Palestinians.