During a swearing-in ceremony at the Western Wall in Jerusalem last Thursday, two soldiers held up a banner that sparked a wave of condemnation by soldiers and civilians alike. The slogan on the banner – "Shimshon [Brigade] does not evacuate Homesh" – referred to the prospect of the soldiers being ordered to evict settlers from an illegal outpost on the site of the former Homesh settlement.

Homesh was dismantled during the disengagement of 2005 but since then settlers have repeatedly returned to the site and erected makeshift homes, asserting their claim of a God-given right to live there, as well as throughout the rest of Judea and Samaria (the West Bank).

On the surface, the IDF's decision to jail the protesting pair suggests a refusal to bow to insubordination within the army's ranks. But set against the wider context of army collusion and co-operation with settler activists, it is hard to regard the verdict as ushering in a new dawn of tough love towards the settler movement. It is more likely that army chiefs disapproved of the troops' particularly public display of support for the settlers, rather than the underlying sentiment they expressed.

Given that the resettlement of Homesh has taken place under the benevolent gaze of the IDF, there is no doubt that the military authorities are still prepared to turn a blind eye to the disobedience of settlers and their supporters – so long it happens in the relative obscurity of the West Bank, rather than in the heart of Jerusalem in full view of both press and public.

I was part of the initial evacuation of Homesh during my army service, and our unit was split by many of the religious members of my brigade refusing to participate – a stance that the Shimshon soldiers this week threatened to repeat. However, instead of standing up to the mutiny, our commanders gave them the kid glove treatment. Their anxiety to avoid an internal confrontation overrode their adherence to army guidelines.

Likewise, every time I witness settlers assaulting and abusing Palestinians in the West Bank, soldiers are always on hand to provide armed cover for the attackers, refusing to intervene on the victims' behalf, and revealing the true level of support the army continues to offer to the settler camp. Such actions speak far louder than the words spouted this week by Major General Avi Mizrahi, who said: "We must ensure that the IDF is not dragged into the political discourse and guard against the creation of factionalism in the military, which is the people's military."

Not only is the IDF dragged into the political discourse day after day, but the army has also been riven by factional splits for years, largely as a result of the infusion of religious dogma into what was, and should remain, a secular institution of the state. As noted by the leader of the New Movement-Meretz party, "instead of religious Zionism adopting the values of the IDF and the country, the IDF and country are adopting the values of religious Zionism, in its nationalist and orthodox version. If this trend continues, the IDF may be transformed from an army of the people to Phalangists carrying religious artefacts."

Furthermore, a Guardian interview with army judge Adrian Agassi reveals in even more detail the influence of religious-nationalist politics on the IDF when it comes to the military's treatment of Palestinians in the occupied territories. Agassi, who has a long history of supporting land confiscations from Palestinian owners, declared that the ancient land of Israel was "given to us by the Bible, not by some United Nations", and that "if we would have named it the State of Jews [rather than the State of Israel], the Arabs would have understood that this land belongs to the Jews".

In his eyes, implanting Jewish settlers across the West Bank is more important than all other biblical commandments, and only when it is done can they have "a promised land and a promised life". With lawyers and judges such as himself at the helm of the military legislature, settler leaders are unlikely to be losing much sleep over the prospect of any serious threat to their wave of illegal construction and land-grabs, despite the slaps on the wrist for the two banner-wielding Shimshon soldiers.

While the rest of Israel fiddles, the West Bank continues to burn – both literally, in the scores of cases of settlers setting fire to the crops and homes of Palestinian farmers, and metaphorically, as the prospects for peaceful resolution go up in smoke the longer the settlers are given free rein to thumb their noses at the law and run riot in the area. On ground level, as well as in the political arena, the authorities seem perfectly content to offer the occasional fig leaf to international pressure to clamp down on the settlers, while never implementing concrete measures to end the overall injustice. Who this charade is fooling is anyone's guess, but the longer it continues, the more certain it becomes that the state's kowtowing to the settlers is driving yet another nail into the peace process's coffin.