I just can not see why the ultra religious in Israel do not want to serve in the IDF. Except perhaps that the ultra religious even before there was a state of Israel did everything they could to stop it. I guess it just snowballed from there.

I can not imagine any halachic reason for them not to serve. Learning Torah --while it i the most  important of all commandments-does not provide an exemption from doing any commandment. הכל יוצאים למלחמת  מצווה אפילו כלה מחופתה