Although the Israeli army’s Conscience Committee can decide to allow exemption from military service, this is usually granted only to those conscientious objectors who refuse to serve on religious grounds. However, according to the UN Human Rights Committee, no discrimination is permitted “among conscientious objectors on the basis of the nature of their particular beliefs” - i.e. whether they are religious or otherwise. Even though Israeli law does allow for exemption on grounds of pacifism, the army’s Conscience Committee frequently rejects pacifists' cases. The authorities deny objectors the possibility of performing alternative civilian service. Conscientious objectors in Israel can be convicted of and imprisoned for the same “offence” repeatedly. In 2003, the UN Working Group on Arbitrary Detention said that this practice flouts the rights of conscientious objectors under international human rights standards which prohibit “double jeopardy”.

Your point was already refuted in the article from amnesty I linked.