Once again in the Middle East, short term gains are trumping long term interests. As the ink dries on the Iran nuclear deal, the bodies are piling up in neighboring Iraq. Many of them are the bodies of Sunni civilians, killed by Shiite militias backed by Iran and allied to the Iraqi Government in the battle against ISIS.

Reports of reprisal attacks against Sunnis by Shiite militias are mounting. Human Rights Watch issued a report in February claiming 'Residents have been forced from their homes, kidnapped, and in some cases summarily executed'. HRW is investigating allegations of a massacre of some 72 civilians in the town of Barwana by militias and SWAT forces. Disturbing videos have circulated on social media of what appear to be Shiite militia members brutalizing and torturing apparently Sunni adversaries in response to ISIS attacks.

In the battle against ISIS, Iraqi forces, Kurdish Peshmerga, and Shiite militias including the Badr Organization and Asa'ib Ahl al-Haq are provided US air cover and billions of dollars in military hardware via the Iraqi Government. That puts the US in de facto alliance with Iran and its proxies, who are accused of war crimes rivaling those of ISIS.

In the predominantly Sunni city of Tikrit, Shiite militias, along with Iranian advisers and even religious imams, led the fight to win back the city earlier this month. The US largely sat that one out, providing air cover to the militias at the end of the battle. Tikrit was previously the scene of the single worst massacre in the current Iraq war, when ISIS militants summarily executed around 1000 Shiites last year. Now in the hands of government forces, it is the scene of renewed accusations of war crimes and executions by mostly Shiite members of the Popular Mobilization Forces against those they accuse of backing ISIS.

As the battle moves towards the Sunni heartland of Anbar province, an ISIS stronghold, which borders Syria and was the site of the strongest insurgency against the Americans in 2004-2006, the reliance on Shiite militias will become even more problematic.

While the Shiite-led armed forces bask in their victory in mixed cities like Diyala and Kirkuk, a Shiite-led victory in Anbar could spark a disastrous escalation of sectarianism, perhaps even ethnic cleansing, while provoking sympathy for ISIS and emboldening the most extreme elements on both sides of the conflict.

The Iraqi Government is hopelessly sectarian and corrupt. In fact, it was the overtly sectarian policies of previous Prime Minister Nouri al-Maliki and his coziness with Iran that gave rise to ISIS. His successor, Haidar al-Abadi, appears to present a genuinely moderate and unifying figure, but Maliki continues to lead his Dawa Islamic Party and the Government is paralysed by sectarian differences.

For Abadi to lead a pacified and united Iraq, the need to include the Sunni population (particularly the tribes) and avoid a further sectarian conflagration in resisting ISIS is paramount. The Iraqi parliament is working on a draft of a highly contentious National Guard bill that would form a unified military umbrella incorporating Sunni entities and tribal forces, possibly including the Kurdish Peshmerga and Shiite irregulars.

But with the battle against ISIS at an important strategic juncture, the bill looks doomed. Why?

One reason is that the tribes are not united. Many of the Sunni tribes which formed the bulwark of the US-backed Awakening Councils that defeated al Qaeda in 2008 are either openly aligned with ISIS or sitting on the fence. They were forcefully opposed to the Maliki Government and are unlikely to join the so-called coalition against their kin. Some Sunni tribal leaders have tried unsuccessfully to put up a resistance to ISIS, calling for more arms and support. Yet ISIS's heavy-handed suppression of this resistance has had a successful deterrent effect.

Moreover, while many Sunni civilians complain about the harsh rule of ISIS, many initially greeted the group as liberators, even facilitating its administration. While that support may have waned as ISIS stepped up its punitive and brutal administration, faced with a choice between ISIS and a sectarian bloodletting at the hands of Iranian-backed forced in a country already mired in sectarian hatred, Sunni civilians may choose ISIS. Recruiting from this pool to the National Guard will prove difficult.

The initiative has also encountered deep opposition among Iranian-aligned factions, which fear their domination over the Iraqi forces will be diluted, and that it may pave the way for a Sunni force that will eventually challenge the central government. Maliki himself and the Peshmerga are understood to be actively trying to derail the process.

Cynics will also point to the recent Iran nuclear deal, suggesting Iran has been given a free hand in Iraq so as not to stymie negotiations. Now that the deal is (more or less) done, Iran has a stranglehold over Iraq, extending its reach to Syria, where the US is pivoting towards its ally Bashar Assad, and Lebanon, where its proxy Hezbollah is strong. With the mythical 'Shia crescent' now almost a reality, it is unlikely Iranian militia members will simply go home to their families once ISIS is done for. Hezbollah's Hassan Nasrallah lauded the nuclear deal as a victory for Iran while the Israeli Prime Minister said 'the concessions offered to Iran in Lausanne would ensure a bad deal that would endanger Israel, the Middle East and the peace of the world.'

If the intention is to stop nuclear proliferation at any cost, the costs must be noted: a more deeply divided Iraq, Iranian hegemony in a torn region, an even more aggrieved Sunni population, and an ideologically emboldened ISIS.

This piece first appeared in the Lowy Interpreter here.