yes, the army's role is to secure its citizens, yes, even the one you dont necessarily like and the ones that behave differently. The IDF is supposed to defend all Israelis and all areas Israel lays claim to, including this holy site.

Additionally, having been there many times myself (though not recently), while plenty of the people who go are mainstream Haredim, many of whom likely did not serve, many are Breslav baal teshuvas and Sefardi chozrim who mostly did serve in the army, in addition to many from the "settlements" community of Datiim who mostly serve. So even if he is right, which he isnt, he is identifying the public incorrectly.