DaasYochid:
I think you misunderstood my kashya. The kashya is that the Gemara says that the Rabbanan are patur because they do not need protection. Apparently, the rest of the city which is not patur, does need protection, despite the Torah learning of the Rabbanan. Had the Gemara said that the Rabbanan and the laymen are equally protected and the Rabbanan are patur because they are contributing to the city’s protection in a different way, then it would be a different story.
As to the rest of your response, do you think that if R’ Moshe thought that there was a grave spiritual danger, he would unqualifyingly write that army service is an inyan gadol? I highly doubt it, and anyway he should have told them that it is assur to go the army instead of just telling them that Yeshiva is better. Since when does R’ Moshe only mention one of two reasons for something in his teshuvos, especially when not mentioning the second one is quite misleading. Let’s say for example that these two guys one day became physically incapable of learning for whatever reason. Well according to you, what would come out is that these guys would join the army based on R’ Moshe’s teshuva, when in fact R’ Moshe would hold that it’s assur to join the army. I don’t see how it is could be that R’ Moshe held that something is assur yet simply wrote that it is an inyan gadol. I guess there’s always the possibility that he was pandering to them and didn’t intend to publish this teshuva for the general populace, and it was post-humously published.