For those claiming the IDF is very hostile to Orthodox Jews, this is simply false. There are Orthodox Jews at every level of authority in the IDF. The entire IDF serves only glatt kosher. They have many staff rabbanim and they do their best to minimize cross-gender interaction within the Orthodox units.
Additionally, no one is suggesting that Torah Study be eliminated, they are only suggesting that only the best should make toraso umnaso, a situation which has been the norm in Klal Yisroel forever.