Torah and militarism are two distinct aspects of Judaism. At times, the two factors converge into one. This is the malchus of David Hamelech, the Torah Warrior. Joshua is also the same idea. At other times, the two factors are separate causing a rift. This is how it was by Yaakov and the rift with Shimon and Levi.
Historically speaking, we are now in the galus of Yaakov. As such, Torah and militarism will remain distinct factors and cause a rift. Neither is wrong. This is why there is currently such a rift in Israel over this issue. The two factions will not integrate into one. Neither is wrong.
The next Torah warrior integration will be in the times of Moshiach. Moshiach will battle the battles of G-d and destroy the wicked.