ISTANBUL, Turkey — The assassination of a high-ranking Syrian rebel commander by an Al Qaeda-linked fighter could spell trouble for the rebels trying to fight the regime of Bashar al-Assad and secure weapons from already skittish Western donors.

A militant with ties to Al Qaeda last week killed a commander in the Supreme Military Council of the Western-backed Free Syrian Army (FSA) in Syria’s Latakia province. The FSA, a loose coalition of mostly Syrian fighters, issued a warning to the extremists to hand over the killer or face an “escalation.”

The disparate groups of Syrian rebels fighting Assad are increasingly involved in clashes with each other over territory, weapons and ideology, damaging an important alliance of opposition forces and making the task of arming the rebels much more complex for Western governments.

US congressional leaders are right now divided over a month-old Obama administration proposal to begin sending light weapons to the opposition, with some worried they could fall into the hands of extremists.

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But the rebel infighting, particularly as it pits the more moderate forces against the Al Qaeda-style fighters battling Assad’s troops, might actually boost the opposition’s chances of receiving help from the West, some experts say.

Al Qaeda-linked groups like Jabhat al-Nusra and the Islamic State of Iraq and the Levant, both fighting in Syria, have excelled on the battlefield. But made up of both Syrians and foreign fighters, they have also struggled to govern and are irking some rebels with their militant ideology.

According to some analysts, a sustained conflict between the FSA and Al Qaeda could lead the international community to coalesce around the FSA, aiding the rebels in their battle against both Assad and the extremists.

“Western involvement changes the incentives” for the rebels, said Aron Lund, a Swedish researcher who studies Syria’s Islamist groups.

“Some FSA figures probably view a conflict with Al Qaeda — or at least the impression of one — as something that would help their public relations work in the West,” Lund said, adding that Al Qaeda-affiliated groups may view the escalation as a way of pulling Western states into the conflict.

Beginning as rag-tag groups with paltry weapons stocks at the beginning of the conflict, when Syria’s army began cracking down on largely peaceful protests across the country in 2011, some FSA brigades are Islamists themselves.

They have taken part in operations with extremists — and Syria’s political leadership has stated it will not turn away from the fight with Assad to battle jihadist groups.

Syria’s civil war is now more than 2 years old, with a loose consortium of opposition fighters battling the well-armed, mechanized forces of the Syrian state. The United Nations said that as of last month, 93,000 have been killed in the increasingly violent conflict.

But other FSA groups are ideologically or politically hostile to extremist factions and see them as alien, power hungry and more concerned with establishing an Islamic state than defeating Assad and his forces.

The ultra-conservative ideology of the Islamists runs counter to that of the revolutionaries that rose up in the beginning, and in a country with a long history of secularism.

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"We don't want our country overrun by Al Qaeda,” said Abdullah Absi, an FSA fighter with the Syrian Martyrs’ Brigade in the northern Idlib province. “We have given our lives for this revolution. When we finish Bashar, we will fight these invaders until they leave."

Jabhat al-Nusra in particular enjoys considerable influence in north and east Syria, though reports suggest it is facing increasing problems with governing.

Nusra fighters have seized control of oil wells in oil-rich eastern Syria, to the chagrin of local fighters and civilians. In Dana, a small town close to the Turkish border, civilians recently demonstrated against the jihadist group’s control of the area. FSA fighters driven from the town have also clashed with foreign-led Islamist militants there.

And in Raqqa, the only provincial capital free of the Syrian government’s control, locals have voiced their opposition to the strict interpretation of Islam enforced by jihadi fighters.

“Syria is our country, not for those who are coming here to make it a battlefield for their own aims,” said Muhammad Raslan, an FSA fighter with Idlib’s Suqour al-Sham brigade.

"What happened recently [the execution of the FSA commander] is so important,” he said. “Because it will uncover those foreign people and prove that they are regime tools to spoil the revolution.”

Joshua Landis, author of Syria Comment, a popular blog, said that while Washington is likely to make good on its promise to arm rebels, the logistics are now more complicated.

The rebels are vulnerable to high-level assassinations. But the FSA may also need weapons and training to keep the Al Qaeda fighters at bay.

“The pressure to keep the FSA from losing to either Assad or al-Nusra will be powerful,” Landis said.

Tracey Shelton reported from Antakya, Turkey.