Joseph & Mentsch: My point is not to point out our questionable history, but the concept of a “Jewish Army” following Halacha is a foreign concept. A Jewish Army follows the halacha, not because a King tell them to follow the halacha or because of the Sanhedrin. They follow it because each individual in that army follows the halacha. As stated, the Army follows the king, not Sanhedrin. If a soldier decides to follow Sanhedrin and not the king, he is killed for Mored B’Malchus.
Menthsch- Yes, hashem performs miracles but ein somchin al haness. After all is said and done, there are halachos that require people to serve in the army; even women! (see Sotah Perek 8) which I am sure the Sanhedrin would also force. So while it is a nice story, the reality is that whoever is required to fight must fight, and as Rashi explains they had officers standing in the back lines with axes in their hand to chop off the legs of people who wanted to run away.
So to summarize, a Jewish Army Al Pi Halacha is an army that each individual upholds the halacha. Al Pi Halacha, this army can contain Men and Women. This Army can fight on Shabbos and when moshiach comes, will also ask Sanhedrin regarding halachic issues and since the king will be Moshiach, there will be no issues. Until then, the army follows the Prime Minister and asks all halachic questions to the chief rabbi.