DaasYochid:
Let me preface my remarks by stating that I am not offering a position on the issue of army service; I am discussing individual mekoros, at this particular moment, the teshuva of R’ Moshe.
I will start by isolating his individual points:
1) Army service is an inyan gadol.
2) Limud Hatorah is better as we see in Bava Basra.
3) The government recognizes this and grants exemptions to those who are learning.
4) Therefore, one who has a passion for learning Torah and to become a gadol in Torah, Hora’ah, and yiras shamayim should go to Yeshiva.
First of all, (and this part is really just stam a kashye on the teshuva, not relevant to what you said) how does the Gemara show that learning is better? All the Gemara says is that the Rabbanan are patur. If anything the Gemara should indicate the oppoisite, because if learning was better (for protective purposes, which is what R’ Moshe seems to be saying) then the entire city should be patur. (You can perhaps give some answer involving hishtadlus, but I’ll leave that up to you.)
His only other point in support of staying in Yeshiva is that the government is maskim. Obviously, then if the government is no longer maskim then this point would cease to be relevant. In such a scenario, all we have left is that Torah is better than Army Service. Now here is where the metzius would be relevant. It is eminently conceivable that a point can be reached where despite Torah being better than army service, the psak could be to to gather arms. I think many people would say that if there was an armed bad guy in the Yeshiva, one should stop learning in order to shot him. (That is an extreme example, intended to illustrate a point.) At this point, it can become very relevant whether the army is spiritually dangerous, as that might override the concerns that are advocating for army service. Therefore it would be instructive for R’ Moshe to discuss it.