Africa's 54th state emerged with high hopes and near unanimous international support on July 9 last year, when Sudan formally split in two after a long, devastating civil war. For decades the black, Christian-animist population in the south had been marginalised by the regime in Khartoum, dominated by Muslim Arabs.

Such was the level of underdevelopment in the south that, by the war's official end in 2005, there were only three surgeons to serve a population of about 10 million and only 4km of tarred road in a territory the size of France.

When the referendum on secession from the north was held in January last year, no one was surprised that 99% of southerners opted for divorce.

By dividing Sudan along a North-South "fault line" it was hoped that many of the conflicts that had historically pitted northerners against southerners would abate, if not be resolved. The south's economy was also expected to finally emerge from the doldrums.

Approaching the first anniversary of South Sudan's independence, the list of problems is almost endless.

Sudan and South Sudan are locked in a number of increasingly bitter clashes over oil, security and borders that threaten to ignite a full-blown war. Last week, Juba accused Khartoum of bombing its territories in Bahr el Ghazal, Unity and Upper Nile states. Khartoum accuses Juba of destroying the oil fields at Heglig in Sudan's Southern Kordofan state, which was seized by the South Sudanese army in April.

In an attempt to avert a renewed north-south war, the UN has threatened sanctions against both sides.

The country is also riven by internal fault lines that have arguably become more rather than less volatile since independence.

Conflicts between different ethnic groups over access to water resources and grazing lands for cattle have occurred for centuries, but in the second half of 2011 alone, clashes in South Sudan's Jonglei state left thousands dead. In one incident, 600 ethnic Lou Nuer were massacred by fighters from the rival Murle community.

In the light of its traumatic start - economic warfare with the North, the emergence of "mini-Kashmirs" on its northern border, renewed internecine conflict - should the international community have been more cautious in signalling its approval of South Sudan's secession in the years leading up to independence?

It is still too early to answer that question.

There can be no doubt that the status quo prior to 2005 was unacceptable for the South. Indeed, it is hard to imagine how war-ravaged and grossly underdeveloped South Sudan could be bloodier or poorer as an independent state than it has been in the past 40 years as an isolated region of Sudan.

Yet the final verdict can't be delivered for at least a generation, by which time we will know how effectively Juba has tackled the divisions - internal and external - left unresolved by secession.

But we can say one thing for certain: today it is less likely that new borders will be drawn in Africa to address intractable fault lines in societies than it was 10 months ago. South Sudan's troubles have hardened international opinion against any further "Balkanisation" of Africa. This is bad news for places such as Somaliland, which craves international recognition and has done nearly everything right in pursuit of independent statehood.

And it is also bad news for the rest of the continent if it stops African decision-makers from considering new ways of addressing the various self-determination movements and divisions which still plague many African states.

The lines drawn by colonial map-makers in Sudan and elsewhere paid scant attention to traditional boundaries and instead sliced through tribes, ethnic groups, even families, in some cases dividing them across two or more states.

In the immediate aftermath of decolonisation, any attempt to untangle the map-makers' legacy would have been a recipe for war and chaos. Built into Africa's DNA is the fear that the slightest change in its "artificial" boundaries will unravel the entire multiethnic patchwork that characterises most African states.

Yet the apparent permanence of Africa's borders exposes the brittleness of many African polities.

Nearly 50 years on, what was once a necessary evil has become a ready excuse for some African leaders to ignore the fault lines within their borders and neglect peoples or groups who may have legitimate claims for special rights.

But they continue to do so at their peril. Some divisions within societies are plainly evident but others are more concealed. If you think differently, you have not been watching the Arab Spring.

In most cases, managing fault lines should not require drawing new borders, as occurred in Sudan, but rather better mechanisms of governance, providing more representative forms of rule for marginalised or disaffected peoples or regions. Secession should always be the last option.

Nevertheless, and despite all of South Sudan's current woes, it seems likely that in future new boundaries will have to be drawn.

• McNamee is deputy director of the Brenthurst Foundation and co-editor, along with Jeffrey Herbst and Greg Mills, of On the Fault Line: Managing Tensions and Divisions within Societies (Profile Books, London).