For a number of years there has been tension between the IDF and the Hesder yeshivot (those that combine Torah study with army service). Eliezer Stern, in charge of personnel, has been spearheading changes to the system that the Hesder yeshivot have protested.
The Jerusalem Post has an article this morning about the latest controversies. In the article, the author claims that the reason that the IDF wants to make changes is to "create a more homogeneous military".
What exactly does that mean? If the IDF wants everyone to be the same, then it means that either the secular soldiers should become religious or the religious soldiers should become secular - an outcome which is impossible to implement, and a foolish one for the army to attempt.
If it means that the makeup of the groups should be equal - well, they already are. It says in the article that out of 40 soldiers, the Hesder yeshivot until now have insisted that 20 should be religious. 50/50 sounds about as homogenous as you can get. If the IDF wants to have more secular soldiers than religious in each group, then "homogeneous" is not the right word.
These changes are in addition to the very problematic inclusion of female instructors for the Hesder soldiers, something that the Rabbis have strenously objected to because of religious reasons.
The overall feeling in the Dati Leumi community (national religious) is that the army is making problems for no reason. The article states, that out of the 1200 Hesder yeshiva boys drafted every year, about 800 go into combat units. It is also well known that a good proportion of those in elite units (I've heard that they make up 50%) are those who wear knitted kipot. (I don't have a link to these statistics - if anyone has I would appreciate the information). So the inclusion of Hesder yeshiva boys in the army is not detrimental to the army - it is a boon. If you consider the fact that overall religious people have more children than the secular, and in future years there will just be more potential candidates for this stream of army service, it seems that forcing these potential draftees to opt out like the Charedim (Ultra-Orthodox) is cutting off your nose to spite your face.