Friend or foe? US lines up with Shiite militias and former Sunni rebels in Iraq

On Monday, Bloomberg carried a story citing two unnamed Obama "administration officials" that asserts that US troops are sharing a base in Iraq's Anbar province with two Shiite militias.
Two questions come to mind: Is it true? And what, if anything, would it mean if it is?
The US says the report is mostly, but not entirely, false. Col. Steve Warren, a Pentagon spokesman told reporters this week that a US condition for sending 450 soldiers to Taqaddum Air Base in Anbar – midway between Islamic State-controlled Fallujah and Ramadi – was the removal of most of the Shiite militias and any Iranian officers or soldiers stationed there. Some liaison officials remain, but the US forces are separated from them and Iraq's government "is helping to coordinate the separation of these two groups," according to Col. Warren. 
It's a reminder of the uncomfortable choices that Iraq has been forcing on the US ever since 2003. The invasion of Iraq ousted Saddam Hussein and helped bring to power Shiite Islamist politicians, many of who had lived in exile under Iranian sponsorship before Saddam's fall. These politicians helped fund the creation of a new Iraqi army and police force that were loaded with Shiite militiamen.
Then there are the Sunni Arab tribesmen that the US later persuaded to switch sides and fight against Al Qaeda in Iraq, which has since evolved into Islamic State. The upshot was that US troops were often working alongside Iraqi Sunnis and Shiites who were trying to kill them yesterday – and might decide to try to do the same thing tomorrow. 
In 2005, I was on a small forward base in Iraq's Anbar province, where US Marines were in the process of taking back the city of Hit from Al Qaeda in Iraq. A group of new Iraqi soldiers arrived on base after being recruited and trained by US forces. The US Marine commander on site was fired up about these new troops who seemed game for a fight. It turned out they were all Shiites from the south; many had Shiite religious slogans on their guns. Some of them spoke warmly of Shiite Islamist politicians who controlled militias. I'd bet good money a lot of them were drawn from the Iran-backed Shiite militias of their time.

Cooperating with Iran

Today, the US is maneuvering particularly tricky waters in Iraq. Prime Minister Haider al-Abadi, a Shiite, is relying on Shiite militias, many of them trained, equipped and advised by Iran, to fight against Islamic State. Since US airstrikes are often coordinated with ground offensives to retake towns like Tikrit, the US is in practice cooperating with Iran. 
Now the US is talking up the need to arm and train Sunni tribal fighters to retake cities like Fallujah and Ramadi and, eventually, the much larger city of Mosul. The odds that none of the fighters who join that effort, if it ever gets up and running, had ever been involved in armed resistance against US forces are very slim.
That hasn't just been a problem in Iraq. In Afghanistan, there were 58 attacks by Afghan soldiers and police on US soldiers and NATO allies, killing 75, in 2012-2013, though the problem has since abated.  But in practice US soldiers have been stationed on bases with Taliban members. Again and again. The reality of exposing US troops to being killed by erstwhile allies could be used to argue against getting involved in the first place. But once the US goes in, exposure - and sometimes cooperation - becomes all but inevitable. 
The Bloomberg story is an opinion piece written by Josh Rogin and Eli Lake in a tone of scandal. "The US military and Iranian-backed Shiite militias are getting closer and closer in Iraq, even sharing a base, while Iran uses those militias to expand its influence in Iraq and fight alongside the Bashar al-Assad regime in neighboring Syria," it begins. Sen. John McCain is quoted: "It’s an insult to the families of the American soldiers that were wounded and killed in battles in which the Shia militias were the enemy. Now, providing arms to them and supporting them, it’s very hard for those families to understand.”
Their point that there's a danger that US troops could be turned on by Shiite militias at some point is a good one. The same goes for Sunni tribesman. That's probably why the bulk of the 450 troops sent to Taqaddum aren't trainers, but there for force protection.
Senator McCain's point is less strong. The US policy remains to work with the government in Baghdad and to try to avoid taking steps that could lead to the full breakup of the country. The government in Baghdad is relying on Shiite militias. While families of lost soldiers might feel insulted, recognizing that fact doesn't provide a solution to the problem. Just as Donald Rumsfeld said in a related context a decade ago, "you go to war with the Army you have. They’re not the Army you might want or wish to have at a later time."

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