halacha - Fighting Wars on Shabbat

As I mentioned in another question, I was reading the Book of Maccabees over Shabbat (I and II).

In the book of Maccabees, it mentions that early on in the struggle, there were a group of Jews hiding out in caves. The Greeks found them and were going to attack them on Shabbat. The Jewish people in the caves, said they would not desecrate Shabbat no matter what, and all got killed.

In response to this, Judah aka Macabeaus, makes a proclamation that it is ok to fight on Shabbat so that they do not all get killed in this manner. Very reasonable.

Centuries later, in the books by Josephus*, Josephus mentions that the Romans were building siege engines, and the Jews would throw down stones to stop the construction. This foiled the Romans, until they started building the siege engines on Shabbat, and noticed that no stones came down on them. Eventually, the Romans only built the siege engines on Shabbat, and the people in Jeruselem got sacked and killed and all sorts of bad things happened. (This was years before the destruction of the temple btw.) Again, a proclamation is made, and the Jews are allowed to fight the Romans on Shabbat.

Later in the Gemorah (Shabbat 19a) (Right before talking about chanukah ironically enough) it is stated that you may not siege a city 3 days before Shabbat. Shamai however states, based on the passuk "Until it is conqureed" that you may siege a city even on Shabbat, until the city is completely taken. (Based on that verse in the Chumash).

Does anyone know what is going on here? Why did the people think they could not fight on Shabbat? Why, 300 years later, did they think so again, and why in the Gemora do they also make the assumption until Shamai says it's ok? Also, why today is it so universally agreed upon that you can break Shabbat when serving in the Army even not during wartime. (If it's ordered/required by the Army to do so)?

• Quote from Josephus:

"The Jewish War" page 40 (I, 156) (Herod's Predecessors)

Pompey himself on the north side was busy filling in the trench and the entire ravine with material collected by the troops. This was a formidable task, as the depth was immense and the Jews interfered from above in every possible way. The Romans would never have reached the end of their labors if Pompey had not availed himself of the seventh day, on which for religious reasons the Jews will not set their hand to any work, raising the level of his earthworks while keeping his men out of all armed clashes; for only in self-defense will Jews fight on the Sabbath. When at last the ravine was filled in he erected high towers on his artificial platform, brought up the engines he had fetched from Tyre, and began to batter teh walls while the stone throwers prevented any interference from above."