That is precisely the problem that the Torah world has with the army.
And that I think is the crux of the problem, In general society there is some effort for everyone to mix together, However in some communities they do not wish this. Its not just the army, There was some school in israel where they didnt want Sefardim because they had different customs and the outcry was either the Charedim were racist or that the hashkfa of the Sephardim would not have worked with the Yeshivish velt Hashgafa.