Rabbi Of Berlin: may I suggest a careful reading of that sugya? 1. We rule AGAINST Rabbi Yehuda: a war to protect Jews is NOT a mitzvah (with regard to osek bmitzvah) and 2. Rashi and the Rambam (perush hamishna) indicate that the only function that it being a mitzvah would have is that if one already was waging war, he would be free from OTHER mitzvos. NOT that one should stop what mitvah he is doing and wage war. On the contrary, osek bmitzvah would free him from waging war.
(see Tos. Yomtov ibid.)