[5] The appointment was criticized by right wing organisations and political figures,[6] including representatives of the Jewish settlers in the West Bank.

[11] The Jerusalem Post called him "the most radical, politically insubordinate officer to have held the position in recent memory", claiming that he "went out of his way to demonize and attack Israeli residents of Judea and Samaria, [claiming] without evidence continuously ... that acts of vandalism against Arab property in Judea and Samaria and inside of the 1949 armistice lines is the work of Jewish residents of the areas".

[12] At the end of his term as commander of the Judea and Samaria Division, Alon stated: "Even today an extremist minority, small in number but not in influence, could bring about a major escalation via acts that are dubbed 'price tag', but amount to terrorism.

In an editorial, the Israeli daily Haaretz called his stance "supremely statesmanlike", and the proof "that not only is he a brave and decorated soldier, but he is also a man of conscience, who fears for the future of his society".

[13] In October 2023, following the Hamas-led attack on Israel, Alon was appointed as the IDF's Commander of the Intelligence Array for Locating the Abducted and Missing Persons.