Funny how times change. When the Bush administration sought permission to transit its Iraq invasion troops through Turkish territory in early 2003, Recep Tayyip Erdogan, Ankara's soon-to-be installed prime minister and his Justice and Development party (AKP) bluntly refused. Their bold defiance of America's will won plaudits around the Arab world, not least from Syria.

With President Bashar al-Assad's regime, not that of Saddam Hussein, now viewed in Ankara as a dangerous enemy, and with the prospect of a bilateral or regional conflict inching closer following Syria's shooting down of a Turkish military plane, Erdogan has swiftly changed his tune. Unwilling to take on Assad by himself, Erdogan turned to the US and Nato for support this week. So much for Turkey's much discussed "strategic realignment".

Turkish commentators have stressed, with unconvincing vehemence, that despite eschewing a direct military response and seeking help from the western powers instead, Erdogan has not "lost face". Mehmet Ali Birand, writing in Hurriyet, said the prime minister's cautious reaction befitted a "serious" state. "Now it is Syria who should be thinking ahead because from now on life will be more difficult … Up to now, a verbal dispute was being experienced. Now it is two enemy nations openly confronting each other."

But Erdogan's vow to target Syrian military formations should they approach their shared border, support opposition forces "at any cost", and do all he can to bring down the Assad dynasty, barely disguises the weakness of Turkey's position. Ankara's twin priorities are both domestic in nature: modernisation and economic growth. Turkey does not want, and cannot afford, a war along its southern border that would jeopardise these aims, further destabilise the Kurdish regions, and seriously compromise its broader regional interests. Assad, presumably, knows this well.

This inherent Turkish weakness was apparent before the Syrian uprising began last year. And it has been aggravated by a string of grave miscalculations by Turkey's foreign policy triumvirate – Erdogan, the foreign minister, Ahmet Davutoglu, and the president, Abdullah Gul – that have left the country largely unprepared to deal with recent events, not least the fall-out from the Arab spring.

Of the three, Davutoglu is the brains. A former professor of international relations dubbed the "Turkish Kissinger" (the nickname is intended as a compliment), Davutoglu coined the AKP's trademark policy of "zero problems with neighbours". In short, Turkey would strengthen its ties with the Arab countries it formerly colonised, act as a good faith conduit to Iran, and maintain a pragmatically positive relationship with Israel. In theory, all this would strengthen Turkey's position as a burgeoning regional power and a hub where the west met the near east.

Some called the policy re-Ottomanisation. And for a while it seemed to be working, as Davutoglu argued in a Guardian interview in 2010. Regarding Syria in particular, old arguments about shared water resources, the disputed border province of Hatay, and Syria's support for anti-Turkish Kurdish militants were set aside. Instead, in 2004, a free trade agreement was signed, visa-free travel was proposed, Gul and Erdogan made high-profile visits, and in 2009 the two countries held joint military exercises. Syrian commanders were invited to inspect Turkish border defences. This open-handedness appears unfortunate now.

So, too, does much else pertaining to Davutoglu's self-interested, blind-eye good-neighbourliness. Relations with Israel went predictably pear-shaped after it shot up a pro-Palestinian freedom flotilla. Post-occupation Iraq under Nouri al-Maliki appears to prefer Tehran's embrace to Ankara's. Iran's nuclear programmers have proven wholly unappreciative of Turkish mediation efforts. And the Kurdish question is as unanswered as ever, witness last week's Turkish air raids inside northern Iraq – another reminder of Ankara's ongoing ineffectuality.

Maybe Egypt, now under Muslim Brotherhood management, will have something to learn from Erdogan's softly softly Islamist approach to Turkey's secular, Ataturkist legacy. Chances are, not.

The Syrian crisis gives Turkey's leaders an opportunity to reorient their country's outlook, on the sounder basis of knowing who your real friends are, not who they might be. The US and Britain fall firmly into the first camp and so do most of the European Nato powers, notwithstanding the anti-Turkish sentiment encouraged by the unlamented Nicolas Sarkozy and some German soulmates. Russia is definitely no friend to Turkey, no more than will be Iran if push comes to bloody shove in Syria.

If growing bands of Syrian refugee "guests" and defectors, unpredictable military provocations, the threat to Lebanon, a ruined commerce and the Damascus regime's generally reckless behaviour are not enough to convince Turkey's leaders where the hope of safety best lies, then perhaps they should focus on one particular issue: Syria's large arsenal of conventional weapons and weapons of mass destruction.

The Christian Science Monitor highlighted the danger this week: "As Syria slides into ever worsening violence and parts of the country begin to slip out of control of the state, Syria's chemical and biological weapons arsenal, air defence systems, and ballistic missiles could be up for grabs – a potential bonanza for radical militant groups and a massive challenge for the west in attempting to check proliferation.

"Hard data on Syria's chemical and biological warfare capabilities is scarce, but the country is believed to have one of the largest chemical agents stockpiles in the world, including VX and Sarin nerve agents. It also has an impressive number of surface-to-surface missiles, such as Scud-Ds which can be fitted with chemical warheads, and modern Russian anti-aircraft missile batteries, including portable shoulder-fired systems."

The prospect that some of these weapons might be used by a desperate regime bent on survival, or may fall into the hands of terrorist groups, however defined, is a daunting one. The ensuing chaos could easily trump what has happened in Libya and the Sahel after the fall of Gaddafi. It poses a potentially existential threat to Turkey and other neighbours. Hopefully, Erdogan and chums now fully understand this.

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