Commanders of the Free Syrian Army (FSA) have reacted with fury to the assassination of a senior FSA officer by a jihadist group, warning that the killing would lead to further violence between the disparate factions battling to oust the president, Bashar al-Assad.

Kamal Hamami, a member of the opposition's supreme military command, was killed and his body mutilated after he was lured to a planning meeting on Thursday with fighters believed to be foreign jihadists in the Jebel al-Krud region, north of Latakia.

The killing – the first internecine targeting of a ranking member of the mainstream Syrian opposition group – follows rising tensions between the exclusively Syrian militia and jihadi fighters, including increasing numbers of foreigners who see the civil war in Syria as part of a global jihad.

Rebel leaders in northern Syria said on Friday that the assassination had shattered trust between the two sides and set off a blood feud.

"This will not go unpunished," said a former officer of the Syrian army who now commands a mainstream opposition militia near Idlib province. "They are trying to assert themselves, to make us bow to them. They need to be taught a lesson."

Since they entered northern Syria in mid-July last year, jihadist groups have become the most effective fighting force in the land, renowned for their prowess on the battlefield and skill in obtaining weapons.

Blighted by ill-discipline and infighting, the FSA has meanwhile struggled to assert itself as its fight against the Assad regime stagnated and more battle-ready militants seized the initiative during raids on military bases that yielded crucial hauls of guns and ammunition.

Recently, however, the jihadists have been accused of the same shortcomings as discipline gives way to power grabs and growing tensions between Syrian and regional al-Qaida leaders.

The main homegrown group, Jabhat al-Nusra, has been undermined by a power struggle between its nominal leader, Abu Muhammad al-Golani, and the leader of the Islamic State of Iraq, Abu Bakr al-Baghdadi, who has led the terror group in its revitalised insurgency against Iraq's Shia-led government.

Baghdadi has attempted to combine his group with Jabhat al-Nusra but was rebuffed in May by Golani, who was reported to have instead pledged loyalty to the al-Qaida leader, Ayman al-Zawahiri. Since then, Jabhat al-Nusra's ranks have split in the same way that the FSA has splintered in the past year.

While it remains a formidable fighting force, it cannot boast the same rigid control over its members and especially over foreign fighters who are increasingly creating their own leadership structures and setting their own rules.

"I've always said that this would become like Anbar," where al-Qaida was driven out in 2006 after earning the ire of local hosts, said a rebel leader in Aleppo. "And I was right. This is now a land of warlords and clans, of foreigners with a perverse form of Islam that share neither our views or goals.

"This is what becomes of a civil war in a place like Syria when help doesn't come the way of the people who need and deserve it."

The spectre of a war within a civil war – mainstream fighters battling foreign fighters – has long been predicted by senior members of established FSA brigades, such as Liwaa al-Tawheed in Aleppo and the Farouk brigades near Idlib and Homs.

For the most part, though, the groups had co-existed, often collaborating on raids and working to the maxim of first winning the battle, then thrashing out how to deal with what remains of the country.

Jabhat al-Nusra members interviewed by the Guardian this year said their leaders, many of whom had fought in Iraq, both against the US army and Sunni tribes, had learned from past mistakes – especially in Anbar, where overplaying attempts to impose and enforce a strict interpretation of sharia law meant they lost the trust of the tribes.

Now, with foreign fighters again taking prominence and employing the same ruthless, uncompromising ways, al-Nusra is losing its bid for containment.

"The war is metastasising in ways that draw in regional and other international actors, erase boundaries and give rise to a single, transnational arc of crisis," says a new report on the Syrian crisis from the International Crisis Group.

"The opposition increasingly resembles a Sunni coalition in which a radicalised Sunni street, Islamist networks, the Syrian Muslim Brotherhood, Gulf states and Turkey take leading roles. The pro-regime camp, encompassing Iran, Hezbollah, Iraq and Iraqi Shi'ite militants, likewise appears to be a quasi-confessional alliance."

The opposition, "not unlike the regime, has acquired a critical and resilient mass of support at least partially immune to the ups and downs of its performance. The large underclass that is its core constituency has suffered such extreme regime violence that it can be expected to fight till the end."