It's overwhelmingly likely that he was murdered by agents of (or on behalf of) the Kingdom of Morocco, but it's unlikely we will ever know for certain exactly what happened. The complicating factor here — as with many murders of political dissidents during the Cold War and the decolonisation era — is to what extent other countries were involved. There are some parallels, for example, with the murder of Congolese independence leader Patrice Lumumba: it has long been alleged that the Belgian colonial authorities, and perhaps the CIA, were complicit in Lumumba's murder. There are almost invariably wildly conflicting narratives and when the secret services are involved, firm evidence is difficult to come by (if you're very lucky, in many decades archives are declassified or legitimate investigations held, and more information emerges.)

Additionally, there's a longstanding tradition of colonial powers being deeply reluctant to talk about the crimes committed during the colonial era and particularly during the chaotic and frequently violent postwar decolonisation process. The British government, for example, has in the last few years been confronted with some unpleasant truths about their actions in Kenya during the Mau Mau insurgency, and is under pressure to release colonial archives that were removed to Britain when the British empire was dismantled. The Radiolab podcast did an excellent episode recently on British war crimes during the Mau Mau insurgency, and the secret archives held at Hanslope Park.

There's a longstanding debate about the French role in Ben Barka's death, and whether it was passive complicity or active involvement. Some say that it was French police officers who abducted Ben Barka; others contend, more moderately, that SDECE knew the abduction was planned and simply did nothing to prevent it. More on that later.

There have been longstanding allegations that the Israeli intelligence services were involved in the death of Ben Barka — and recently, more evidence has emerged which appears to support those claims.

In the 1960s, Mossad had a working relationship with the Moroccan secret services (as part of a wider effort to build relationships with certain Muslim countries in the Middle East and North Africa, as a bulwark against Gamal Abdel Nasser's Egypt.) Ben Barka was a key opponent of Hassan II's regime, and according to some sources the regime requested Israeli help in silencing him.

This is how Dan Raviv and Yossi Melman — two reporters who co-wrote a pair of histories of Israeli intelligence — recounted the Israeli role in the Ben Barka murder in 2012 in Spies Against Armageddon:

The Moroccans demanded that the Mossad help them hunt for Mehdi Ben Barka, a charismatic opposition leader who tried to stir up a revolution in his country and was forced into exile in Switzerland. The head of the secret police, General Mohammed Oufkir, then explicitly asked [Mossad director Meir] Amit to have Ben Barka killed.

[...]

Amit consulted with [Israeli prime minister Levi] Eshkol, and they decided on a compromise. The Mossad would give non-lethal assistance, helping the Moroccans locate Ben Barka and persuading him to come to Paris — but that would be all.

Mossad operatives, posing as a film crew, found the Moroccan dissident in October 1965 and invited him to meet them in a fashionable cafe on the Left Bank. General Oufkir was waiting there, with a team that included Moroccan agents and French mercenaries.

Oufkir's men spirited away Ben Barka and tortured him in a villa. He was then either shot or stabbed, reportedly by Oufkir himself. A senior Mossad man based in Paris was apparently nearby, maintaining contact out of some strange sense of courtesy.

Recently, two Israeli reporters, Ronen Bergman and Shlomo Nakdimon, published a lengthy account of the Israeli-Moroccan intelligence relationship and the Ben Barka operation, based on Mossad documents (the 'Baba Batra file') they obtained and interviews with former senior Israeli intelligence officers, which seems to confirm the broad strokes of Raviv and Melman's account, but differs in some key details: they don't place Oufkir in the room (or in France) during the abduction; instead, they identify Ahmed Dlimi, his lieutenant, as the senior Moroccan figure on the ground.

More surprisingly, they claim a completely different manner of death, and claim that Ben Barka's death was unintentional (or at least premature); that he died while being tortured by the Moroccans. Here's their account of the abduction:

The Moroccans, accompanied by mercenaries from French intelligence and local police, were waiting for the arrival of Ben Barka in the City of Lights. Indeed, on the morning of October 29, Ben Barka arrived from Geneva, equipped with an Algerian diplomatic passport.

Ben Barka rushed to Brasserie Lipp, a known meeting place on the banks of the Seine, where he was to dine with a French journalist. He did not know that the journalist was bait set by the Moroccan intelligence to lure him into a trap. According to Dr. Ben-Nun's research, this was the Mossad's idea.

At a bend in the road before the restaurant, two French policeman — both the mercenaries in the pay of Dlimi — asked him to accompany them. A stunned Ben Barka was quickly led to a rented apartment in a suburb south of Paris, where Dlimi began to torture him severely.

On November 1, when Ben Barka was still alive, Dlimi asked the Mossad in Paris to provide by the end of November 2 a toxin and two more foreign passports, shovels and "something to disguise the traces."

Previously, there were different versions of what happened then: some argued that the station chief Rafi Eitan cabled Meir Amit a request for instructions, but before a decision could be made on whether to provide or refuse the poison, the issue became irrelevant. Others argued that the Mossad complied with the request and the poison arrived in Paris, but it was no longer necessary.

Either way, in an apartment in Paris, Dlimi and some of his aides tortured Ben Barka, competing to see who would be more vicious. What began with cigarette burns, became electric shocks and ended with repeatedly forcing the victim into a tub of stagnant water, with Ben Barka on his knees.

Dlimi had not intended to kill Ben Barka, at least not at that stage, but only gather information about the underground and force him to sign a confession stating that he had intended to overthrow the king.

The late Mossad agent Eliezer Sharon replayed to us before his passing what he had heard from the Moroccans after the fact: "They filled a bathtub with water. Dlimi grabbed his head and wanted him to reveal information. Every time Ben Barka stuck his head out of the water, he spat and cursed the king. They held his head under the water a little too long, until he turned completely blue."

The Bergman and Nakdimon story suggests that the French involvement in the case was 'mercenary'; that it was police and intelligence officers acting without official sanction — and that their involvement was the catalyst for the political scandal mentioned in the wiki article you quoted:

The French team who participated in the operation very quickly leaked to those close to then-French president Charles de Gaulle that the Moroccan security services had abducted and murdered the political leader in the heart of Paris. The French president reacted furiously: He fired a large part of the leaders of his country's intelligence services, dismantled the SDECE, France's foreign intelligence agency, and demanded that King Hassan hand over Oufkir and Dlimi. When the king refused, de Gaulle severed diplomatic relations with Morocco.

As I said: these stories are always difficult to untangle, and there are always blank spots. The Bergman and Nakdimon story, however, is the most current and rigorously-sourced account of the operation I've read (which is partly linked, admittedly, to the fact that the Ben Barka scandal was a much bigger deal in the Francophone world than in the Anglophone one — if you can read French, you'll find much, much more analysis and commentary out there), and it makes a compelling case that it was the Moroccan secret service, supported by Mossad, who were the key actors in Ben Barka's death.

Edit: for clarity.