Uhuru Kenyatta, after winning a seven-point victory in the March 4 presidential election, will be sworn in later this month as Kenya’s fourth post-independence president.

But he’ll do so with a significant cloud hanging over his head — an indictment from the International Criminal Court on charges of crimes against humanity stemming from the last election in 2007, which precipitated two months of post-election violence that followed allegations of fraud in the narrow victory of incumbent Mwai Kibaki over challenger Raila Odinga.

What’s more, Kenyatta’s running mate, the next vice president of Kenya, William Ruto, is also a defendant on similar charges.

But Kenyatta, who comes from the Kikuyu ethnic group, and Ruto, who comes from the Kalenjin ethnic group, were on opposing sides five years ago, with Kenyatta backing Kibaki and with Ruto backing Odinga.

Those differences weren’t enough to stop Kenyatta and Ruto from joining forces this time around. Their partnership led to yet another defeat for Odinga and, this time around, the election result met with none of the civil turmoil that followed the previous election.

Nearly everyone in Kenya want to move beyond the 2007-08 violence.

Moreover, the ICC’s case against Kenyatta remains an evidentiary weak case by the standard of other ICC efforts. The ICC’s prosecution has already intruded bluntly into Kenya’s domestic politics and governance in a way that the entire Kenyan political elite opposes and that risks the court’s own legitimacy in sub-Saharan Africa, and the Kenyan people — in a free and fair vote — have elected Kenyatta their president, ICC charges or not.

The ICC indictments threaten to transform Kenya into somewhat of a pariah state — the European Union has pompously declared before the election that it would only engage in ‘essential conduct’ with Kenyatta in the event of his presidential victory, and U.S. secretary of state for African affairs Johnnie Carson was widely criticized for trying to subtly ‘warn’ Kenyans to make its choice carefully because it would have ‘global consequences.’

Kenya remains a key regional ally in the otherwise tough neighborhood east Africa, so Western governments will need to walk a tight diplomatic line, notwithstanding the ICC’s role:

A diplomatic fumble in dealing with Kenyatta could damage ties with a nation that has helped quell militant Islamists in the region and push a traditionally pro-Western state closer to China and other emerging powers hungry for openings in Africa.

Kenya’s supreme court earlier this year pointedly cleared Kenyatta, the son of Kenya’s first president Jomo Kenyatta, and Ruto to run in the election despite the ICC charges.

If that weren’t enough, the ICC may have already warped Kenyan politics by boosting Kenyatta’s bid through a sort of rallying effect — giving Kenyans a nationalist cri de coeur in a country where politics are still largely fought and won on ethnic lines.  

The post-colonial tut-tutting from Western powers may be chief among the reasons that Kenyatta overtook Odinga’s initial poll lead to win a first-round victory in the presidential election.  Although Odinga took a few swipes at Kenyatta’s legal troubles — in the first presidential debate, Odinga said that it ‘will pose serious challenges to run a government by Skype from the Hague, it is not practical’ — Odinga begrudgingly agreed, along with much of Kenya’s political elite, that the charges should be handled in Nairobi, not in the Hague.  When the charges were referred to the ICC in 2010, both Kibaki’s administration and the National Assembly opposed the move, and the National Assembly even voted to remove Kenya as a signatory to the Rome Statute governing the ICC.

Kenyatta has argued that Kibaki and Odinga bear as much blame for the 2007-08 violence, and urged that Kenya’s democratic process should settle the issue:

For now, the ICC prosecutors say that Kenyatta’s case will move forward with a trial set to start in July, and Kenyatta has agreed so far to cooperate.  But that doesn’t mean that the case should move forward — the ICC dropped similar charges against Francis Muthaura, a cabinet secretary and key Kibaki ally earlier this year, and its evidentiary case against Kenyatta, while stronger than the case against Muthaura, remains less than convincing.

Kenyatta is charged with funding and inciting violence, particularly in Naivisha and Nakuru district, though it’s not clear exactly what his role was in the violence.  Ultimately, when Kibaki and Odinga reached a power-sharing deal for Kibaki to retain the presidency and Odinga to become prime minister, Kenyatta became a deputy prime minister and finance minister in the new government, so he obviously wasn’t so toxic to Odinga in early 2008.

Even assuming arguendo that Kenyatta bears some guilt for the 2007-08 violence, his transgression seems less like that of Uganda’s Joseph Kony, head of the Lord’s Resistance Army, or former Côte d’Ivoire president Laurent Gbagbo, who crimes are well document.

The more relevant analogy may be Gujarati chief minister Narendra Modi (who has been accused of doing little in 2002 to stop a violent Hindu retribution that led to the death of over 1,000 Muslims in Gujarat) — Modi, who’s been reelected three times in the past decade, is now a chief candidate to become India’s prime minister in 2014, and the European Union and the United States have backed down on its previous stance refusing to issuing Modi a visa.

But more widely, the ICC risks tarnishing its own reputation by pushing ahead with Kenyatta’s prosecution — if the case goes forward and Kenyatta wins, it will call into question not only the judgment but the legitimacy of the court.  Even the United States has argued that there are insufficient checks and balances on ICC prosecutors.

That’s especially true in light of the fact that in nearly a decade of operation, despite initial investigations into conduct on five continents, the ICC has indicted 30 individuals in seven countries, all of them African — and among that group, all but three indictees and one country (Libya) hail from sub-Saharan Africa in particular.  That’s led to grumbling in Kenya and beyond that the ICC is just another neocolonial institution established to antagonize Africa, which could ultimately destroy the court’s credibility in the long run:

All of which is not to deny that the ICC may have an Africa problem, but the problem is that its largest constituency seems to have little or no confidence in the ability of the court to deliver the kind of protections it was designed to deliver, in an equitable way. I would posit that the efficacy of a judicial system lies in the confidence that those potentially judged by it have in the system’s ability to mete out justice.