The image of Mali has long been a gentle one. It is a land of magical music and mouth-watering mangoes, of mud mosques and medieval manuscripts. A country dripping with history and culture that was slowly forcing its way on to the tourist map for Western visitors. Now, following the intervention of French warplanes nine days ago, it will be more associated in most people's minds with Islamic militancy.

This is a tragic twist for a people whose faith revolves around the more tolerant strands of Sufism. For all its poverty, Mali has traditionally been open to outsiders. It is a nation where women are prominent and musicians more closely entwined with everyday life than perhaps any other place on earth. Music has long been part of the social and political fabric, from praise singers who, for centuries, passed on the oral history to the state-funded bands used to bond the nation after independence.

When I first went there almost a decade ago, it was for the famous Festival in the Desert, some 50 miles from Timbuktu and a symbol of reconciliation after a previous Tuareg uprising. It took three days to get there; Westerners reaching the event were treated like old friends. Days were spent sheltering from fierce sun in tents, chatting over cups of sweet tea and biscuits. At night, those amazing musicians who have taken Malian music around the globe performed in front of turbaned tribesmen on camels while burning braziers lit up the desert. An unforgettable experience.

Where once there was music and dancing, today there is misery and deprivation. When I visited Timbuktu, I was beckoned by an old man into the 14th-century mosque, then shown around the city by a teenage boy. Handing him a tip, he shared it with others. Now this fabled city lies at the heart of the fundamentalist badlands in which uncovered women are whipped, couples stoned to death for adultery and children segregated by sex. There are gruesome tales of suspected thieves having hands sawn off. Villages have been emptied as families flee marauding militia, many from outside the country. Perhaps most incredibly, the music that so defines this country is banned from two-thirds of its territory.

France, which had been trying to marshal a supposedly African-led intervention for months, had no option but to act. Not just because there are 6,000 citizens in its former colony. But because the Islamists were heading south towards the main population areas. They were just one hour away from the second city – and had that fallen, the entire country could have collapsed into their control. This would be hideous for Mali, disastrous for the region and highly worrying for the West, especially given the number of Malians in France.

In Bamako, there is strong support for the French action; critics who see it as some kind of neo-colonialist invasion appear absurdly ill-informed. Most Malians are fearful of the militants seeking to impose their interpretation of Islam on a people for whom it is so alien. Bassekou Kouyaté, one of Mali's most famous musicians, typified the mood when he told a newspaper he was off to buy a French flag to fly in front of his house.

On another trip to Mali, I was welcomed into Bassekou's house where his band played one of the most astonishing concerts I have seen. It was powerful and contemporary, yet, like so much Malian music, recognisably in touch with its roots.

I last saw him in September, when he joined the Africa Express train taking music around Britain and played with Paul McCartney, Baaba Maal and Damon Albarn. Whether from north or south, all the Malian artists used the opportunity to speak about the tragedy that had befallen their country yet was being ignored by the world.

Now the world has woken up. Strong countries, however, do not collapse like a pack of cards – not even those on the fault line between the Arab and African worlds. The government may have been democratic, but it was also tired and unpopular. This is one of the world's poorest places, propped up by aid and pockmarked by unemployment, especially among the young. Many older people in this conservative nation were concerned by changing social mores. The army, meanwhile, was renowned for incompetence and riddled with corruption.

Long-held Tuareg dreams of independence turned into a dystopian nightmare after the separatists were shoved aside by religious fanatics. Externally, the view is of the Sahel region cursed as the latest front in the global war on terror. Militants have poured in from as far afield as Pakistan, along with armed gangs from neighbouring nations, provoking fears the struggle could ignite the wider region. Even Nigeria – struggling to control its own Islamic terror group which is thought to be involved in Mali also – could become engulfed. This emerging African superpower is a key Western oil supplier; the economic shock waves would be devastating.

Viewed internally, however, this is too simplistic. Not only are the events rooted in often long-running tribal, regional and personal grievances, albeit inflamed by more modern issues such as drug-running and kidnapping tourists. But, at heart, this is really a cultural conflict – between those embracing democratic values and those seeking the certainty of theocracy. It is a struggle between the future and the past, between unity and division, between tolerance and repression, between singing and silence. Only in Mali would musicians be on the front line of a fight for the salvation of a nation.

Ian Birrell is co-founder of Africa Express, which brings together African and Western musicians. twitter.com/@ianbirrell