As the international coalition of countries continues to fight the Islamic State of Iraq and Syria (ISIS), some unlikely alliances are proving effective. While both the U.S. and Iran have said they are not coordinating efforts, Supreme Leader Ayatollah Ali Khamenei's backing of Kurdish and Shiite militias is a key component to the fight.

But CBS News senior security contributor and former CIA deputy director Michael Morell said that de-facto relationship comes with some possible serious consequences.

"There's a real risk here that over the long run we can defeat ISIS in Iraq, but we might hand Iraq to the Iranians, in a diplomatic sense," he said Tuesday on "CBS This Morning."

U.S.-backed Iraqi ground forces have not proven nearly as effective as the combination of coalition airstrikes and Kurdish and Shiite Muslim militias, which have clawed back significant territory from ISIS in northern Iraq of late.

"Iran is, I think, the most effective fighting force inside of Iraq. They have trained, they have supplied 100,000 Shiite militia, that compares to 50,000 Iraqi security forces who are not very effective," Morell said. "The Iranians are actually on the ground fighting with those Shia militia. "

Iranian officials have acknowledged that members of its elite Quds force, a military special forces division, are fighting inside Iraq.

On "Charlie Rose," U.S. Director of National Intelligence James Clapper said the Quds force could help defeat the terror group.

"In an advisory capacity, they brought in large amounts of weaponry, they fly UAVS over Iran. So, yes, they have a very robust commitment to the fight against ISIL in Iraq," he said, using an alternate acronym for the militant group.

Morell agreed.

"They have sent a lot of heavy weaponry in. They are providing a lot of funds. So they are the most effective fighting force there today," he said.

Inside Iraq, the government faces an important challenge. Prime Minister Haider al-Abadi has reached out to Iraq's minority Sunni population, which was largely viewed as marginalized under former Prime Minister Nouri al-Maliki.

Morell said that while the battle against ISIS seems to have united the two Islamic sects for the time being, the centuries-old rift could reignite at any time.

"As the Shiite militia and the Iranians push into Sunni areas, I think one of the things that you're going to see, given this Sunni-Shiite tension, is you're going to see Sunni Arabs actually come over to the side of ISIL. So from propaganda perspective, this will be a bonanza for ISIL," Morell said.

Morell also spoke about new details emerging on the recently unmasked ISIS' executioner Mohammed Emwazi, also known as "Jihadi John." In interviews with an advocacy group in 2009, Emwazi said he told British security officials that the 9/11 attacks, and the 7/7 transport bombings in London, were "wrong."

"A lot can happen in five years, so I think that's the first thing to remember. I think the second thing to remember is we don't really know he got radicalized. The radicalization process is a very personal one," Morell said.

The advocacy group, which said it knew Emwazi as a "beautiful" young man, has suggested that the attention of British security forces, at least in part, drove him toward ISIS.

"I don't believe that. I think it's much more likely that they (ISIS) saw the jihadi potential in him and that they played a role in driving him toward this."