Can I serve under a non-religious commander in the IDF? Does this bring up Halachic and moral issues? If you cannot accept witness testimony of someone who breaks Shabbat how can you serve under him?
Since the beginning of the IDF, PM David Ben-Gurion ordered that the Israeli army be run according to halacha, to enable the entire nation, including the religious, to serve together. To this day, no exercises nor target practice etc. but only life-threatening activities, are done on Shabbat, all food must be kosher, there must be a mezuza on every door, all soldiers are given ample time to pray on each respective day, and all orders must be in consonance with halacha. The only heartbreaking exception was the one-time order 16 years ago to uproot Jewish settlers from Gush Katif, which was tragic from many aspects, but even then, any soldier who didn't want to participate, was given the option to serve elsewhere. Who can or can't give testimony in Beit Din is dictated by the Torah, and accordingly is a unique issue with unique laws (e.g. even women can't testify), but one can surely obey and rely on a non-religious medical specialist, and similarly, a military specialist. In addition, if soldiers don't follow orders, we obviously will not have an army, and the dangerous ramifications are obvious. The holiness of saving even one life supersedes the sanctity of Shabbat or one's fasting on Yom Kippur, so how much more so must we follow the orders of the army when legally they can never contradict any mitzvah, and they're out to save the entire nation of Israel. May God watch over them as they and He watch(es) over us.