The destruction of Syria is now in full flow. What began as a popular uprising 17 months ago is now an all-out civil war fuelled by regional and global powers that threatens to engulf the entire Middle East. As the battle for the ancient city of Aleppo grinds on and atrocities on both sides multiply, the danger of the conflict spilling over Syria's borders is growing.

The defection by Syria's prime minister is the most high-profile coup yet in a well-funded programme, though unlikely to signal any imminent regime collapse. But the capture of 48 Iranian pilgrims – or undercover Revolutionary Guards, depending who you believe – along with the increasing risk of a Turkish attack on Kurdish areas in Syria and an influx of jihadist fighters gives a taste of what is now at stake.

Driving the escalation of the conflict has been western and regional intervention. This isn't Iraq, of course, with hundreds of thousands of troops on the ground, or Libya, with a devastating bombardment from the air. But the sharp increase in arms supplies, funding and technical support from the US, Saudi Arabia, Qatar, Turkey and others in recent months has dramatically boosted the rebels' fortunes, as well as the death toll.

Barack Obama has so far resisted the demands of liberal hawks and neoconservatives for a direct military assault. Instead he's authorised more traditional forms of CIA covert military backing, Nicaragua-style, for the Syrian rebels.

The US, which backed its first Syrian coup in 1949, has long funded opposition groups. But earlier this year Obama gave a secret order authorising covert (as well as overt financial and diplomatic) support to the armed opposition. That includes CIA paramilitaries on the ground, "command and control" and communications assistance, and the funnelling of Gulf arms supplies to favoured Syrian groups across the Turkish border. After Russia and China blocked its last attempt to win UN backing for forced regime change last month, the US administration let it be known it would now step up support for the rebels and co-ordinate "transition" plans for Syria with Israel and Turkey.

"You'll notice in the last couple of months, the opposition has been strengthened," a senior US official told the New York Times last Friday. "Now we're ready to accelerate that." Not to be outdone, William Hague boasted that Britain was also increasing "non-lethal" support for the rebels. Autocratic Saudi Arabia and Qatar are providing the cash and weapons, as the western-backed Syrian National Council acknowledged this week, while Nato member Turkey has set up a logistics and training base for the Free Syrian Army in or near the Incirlik US air base.

For Syrians who want dignity and democracy in a free country, the rapidly mushrooming dependence of their uprising on foreign support is a disaster – even more than was the case in Libya. After all, it is now officials of the dictatorial and sectarian Saudi regime who choose which armed groups get funding, not Syrians. And it is intelligence officials from the US, which sponsors the Israeli occupation of Syrian territory and dictatorships across the region, who decide which rebel units get weapons.

Opposition activists insist they will maintain their autonomy, based on deep-rooted popular support. But the dynamic of external backing clearly risks turning groups dependent on it into instruments of their sponsors, rather than the people they seek to represent. Gulf funding has already sharpened religious sectarianism in the rebel camp, while reports of public alienation from rebel fighters in Aleppo this week testifies to the dangers of armed groups relying on outsiders instead of their own communities.

The Syrian regime is of course backed by Iran and Russia, as it has been for decades. But a better analogy for western and Gulf involvement in the Syrian insurrection would be Iranian and Russian sponsorship of an armed revolt in, say, Saudi Arabia. For the western media, which has largely reported the Syrian uprising as a one-dimensional fight for freedom, the now unavoidable evidence of rebel torture and prisoner executions – along with kidnappings by al-Qaida-style groups, who once again find themselves in alliance with the US – seems to have come as a bit of a shock.

In reality, the Syrian crisis always had multiple dimensions that crossed the region's most sensitive fault lines. It was from the start a genuine uprising against an authoritarian regime. But it has also increasingly morphed into a sectarian conflict, in which the Alawite-dominated Assad government has been able to portray itself as the protector of minorities – Alawite, Christian and Kurdish – against a Sunni-dominated opposition tide.

The intervention of Saudi Arabia and other Gulf autocracies, which have tried to protect themselves from the wider Arab upheaval by playing the anti-Shia card, is transparently aimed at a sectarian, not a democratic, outcome. But it is the third dimension – Syria's alliance with Tehran and Lebanon's Shia resistance movement, Hezbollah – that has turned the Syrian struggle into a proxy war against Iran and a global conflict.

Many in the Syrian opposition would counter that they had no choice but to accept foreign support if they were to defend themselves against the regime's brutality. But as the independent opposition leader Haytham Manna argues, the militarisation of the uprising weakened its popular and democratic base – while also dramatically increasing the death toll.

There is every chance the war could now spread outside Syria. Turkey, with a large Alawite population of its own as well as a long repressed Kurdish minority, claimed the right to intervene against Kurdish rebels in Syria after Damascus pulled its troops out of Kurdish towns. Clashes triggered by the Syrian war have intensified in Lebanon. If Syria were to fragment, the entire system of post-Ottoman Middle East states and borders could be thrown into question with it.

That could now happen regardless of how long Assad and his regime survive. But intervention in Syria is prolonging the conflict, rather than delivering a knockout blow. Only pressure for a negotiated settlement, which the west and its friends have so strenuously blocked, can now give Syrians the chance to determine their own future – and halt the country's descent into darkness.

Twitter: @SeumasMilne