Mohammed Dajani knew he was on sensitive ground when he took a group of students to visit the site of the Auschwitz concentration camp in Poland in March. But it took the furore that followed to make the Palestinian academic realise that he had entered a political and psychological minefield.

Dajani resigned from his post at Jerusalem's Al-Quds University this week after failing to win the unequivocal support of his employers in a row which highlighted the darkest taboos of the conflict with Israel and each side's enduring sense of victimhood.

The visit to the concentration camp was part of a project to study the Holocaust and teach tolerance and empathy. "It is about understanding the other," Dajani told the Guardian during a conference in the Qatari capital, Doha. "You need to understand the other because reconciliation is the only option we have. And the sooner we do it the better. Empathising with your enemy does not mean you sanction what your enemy is doing to you."

Organised in conjunction with three other universities, one German and two Israeli, the project also arranged for Israeli students to meet Palestinians living in refugee camps.

Dajani faced abuse, intimidation and death threats over the visit. Al-Quds dissociated itself from the project but defended his right to be involved. It insisted he had not been dismissed and supplied him with bodyguards. But in the end it accepted his resignation.

Implacable in the face of the uproar, he rejected accusations that he intended to promote the Zionist narrative of the conflict rather than respecting the primacy of the Nakba ("catastrophe" in Arabic) – the flight, expulsion and dispossession of hundreds of thousands of Palestinians that was the price of Israel's independence in 1948.

"I felt it was important for us Palestinians to learn about this event first because it is historically wrong to deny it and also because it is morally wrong to ignore it," he said. "I felt I should not be a bystander but take a stand. I lived in a culture where the Holocaust was not viewed in depth and was used artificially, linking it to the Nakba. We never learned about its impact, its lessons, why it happened, to whom it happened. It was always in the background as if it was a taboo topic."

Dajani, 66, is from one of Jerusalem's most famous families. In the 1960s he fought with Yasser Arafat's Fatah movement in Lebanon but abandoned the armed struggle to study in the US. In 1993, when Israel and the Palestine Liberation Organisation (PLO) signed the Oslo accord, taking the historic step of recognising each other, Dajani returned home and helped to train Palestinian civil servants.

Later he set up a pioneering Israeli studies programme at Al-Quds. Tackling the Holocaust, he said, grew out of his realisation that Arab attitudes had been distorted by hostility to Zionism and to the state of Israel – the creation of which owed so much to western guilt over the fate of the Jews during the second world war.

Propaganda that conflates antisemitism with opposition to Israel has also played a role. Israel's foreign minister, Abba Eban, famously talked about the country's "Auschwitz borders". Menachem Begin, the prime minister who invaded Lebanon in 1982, described Arafat "cowering in his bunker" in Beirut like Hitler in Berlin.

Wartime collaboration with the Nazis by the Palestinian leader Haj Amin al-Husseini was another factor. Few books on the subject appeared in Arabic. In 1984 Mahmoud Abbas, now the Palestinian president, denied the Holocaust in a doctoral thesis he defended in Moscow.

But attitudes change. This April, Abbas called the Holocaust the "most heinous crime" in modern history. Other Palestinians agree but still oppose Dajani's emphasis.

"The Holocaust was a terrible crime," the PLO official Husam Zomlot commented at the Doha conference. "But the Nazis were responsible for it. The Palestinians had nothing to do with it. The Israelis were responsible for the Nakba."

The 27 students who went to Auschwitz came under pressure before and after the trip. Two dropped out at the last minute.

Dajani said it was profoundly disturbing to be in the place where 1 million people, the vast majority of them Jews, were systematically murdered. When a Palestinian woman who had been jailed in Israel asked him the meaning of the slogan arbeit macht frei (work sets you free) over the camp entrance, she discovered that the SS commander had said that there was only one way out – through the chimneys of the crematoria.

"I told her that that is one way of making a distinction between our Nakba and their Holocaust," Dajani said. "In our Nakba you can negotiate, you can walk out of the prison. In their Holocaust there was no negotiation. There were victims and perpetrators and there was no dialogue or way out except through the chimneys of the crematorium.

"When we Palestinians look at the Holocaust we impose it on our own suffering. We see a Nazi guard tower and we think of the Israeli guard tower or barbed wire. But Jews see the "final solution" and an attempt to annihilate them as a people. One of my students thought Hitler had gathered the Jews in these camps in order to ship them to Palestine! This trip was highly emotional – and a very educational experience."

Misunderstanding played some role in the row. An article in an Israeli newspaper about the Auschwitz trip was mis-translated into Arabic. And the timing was unfortunate – just as the last round of US-brokered peace talks was on the brink of collapse – even though the project had begun long before.

There were angry objections from supporters of the Boycott, Disinvestment and Sanctions (BDS) movement, which rejects any kind of Palestinian "normalisation" with Israel.

Dajani, who founded a movement called Wasatia (Centrism) said he remained committed to a two-state solution to the conflict. "I knew it was a taboo and that it would be negatively received," he said. "But I did not realise how deep and how explosive it was for the Palestinian psyche. It was like walking in a minefield."

On the Israeli side, awareness of the Nakba has grown in recent years thanks to myth-busting historical research and to the work of an organisation called Zochrot, though that does not translate into Jewish support for the return of Palestinian refugees.

Dajani said there was an imbalance of empathy between the two sides. "If I wanted to make a comparison, I would say that the Jews know more about the Palestinians than the Palestinians know about the Jews. Because there is an asymmetry of power it is easier for those with power to show empathy than it is for the occupied, who are powerless. It is harder for the victims to feel sympathy when they are suffering on a daily basis. On their side they don't face the same pressures."