Yhyjyk

I have read about the ways to mitigate the "mob rule" or "tyranny of the majority" here, but is it a practical issue in the first place ?

Has it been observed in a direct democracy context or in a referendum under non direct democracy ?

In other words, is there an example in history where a people officially voted for the destruction of a minority ?

In 1879, California held a referendum on Chinese exclusion that passed the all-white electorate by a margin of 154,638 for to 883 against. It was later codified into law by elected representatives, both in the California Constitution as well as Federal Law.

In other words, 99.4 percent of the all-white California electorate voted to exclude all Chinese immigrants from the state forever. It was a remarkably unanimous show of nativist hostility toward a single immigrant group. Hatred of Chinese immigrants — the “indispensable enemy” — had become the one issue upon which white working-class Californians of all nationalities, religions, ethnicities, and political parties could agree.

In 1901, Alabama held a state-wide referendum calling for a constitutional convention with the express purpose to "establish white supremacy in this State". The resulting convention ultimately not only disenfranchised almost all African Americans in the state, but most poor white people also.

The second one may be a bit borderline, since it involved not only a massive amount of voter fraud in order to get passed, but the poor whites who were also disenfranchised were told that it was the only way to keep from being disenfranchised by the wealthy gentlemen who ran the convention. More information

In 1910, Okalahomans passed Oklahoma Initiative 10 that required proof of literacy in order to vote. There was a grandfather clause included allowing anyone to vote who was also entitlted to vote prior to January 1, 1866 ensuring that the qualification only applied to African Americans. The vote was 56% for to 44% against.

In 1963, the California Legislature passed the Rumford Fair Housing Act which attempted to prohibit racial discrimination by realtors and owners of apartment buildings built with public assistance. In response, the California Real Estate Association and other real estate groups helped place Proposition 14 on the November ballot, essentially nullifying the Rumford Act and ensuring a "right to discriminate" for housing sales and rentals, and was passed the same day Lyndon Johnson was elected president with almost 2/3 (65%) of the vote.

I think your requirements are just too restricting to find many examples.

There aren't that many cases of direct democracy in the first place, and "voted for the destruction of a minority" is a very high bar. There's a reason that people talk about the singularity of the Holocaust; there aren't very many places in time where people had 1) the desire and 2) the means to exterminate an entire people. A lot of discrimination is about exploitation, exclusion, or subjugation, not necessarily about annihilation.

I know of at least one example of violations of basic human rights in a direct democracy though. The people of Switzerland voted with 57% to forbid the building of minarets (which goes against the freedom of religion).

We can also see tyranny of the majority in non-direct democracies, such as the support of Germans for the NSDAP, the support of slavery and Jim Crow in the US, restrictions of basic human rights for LGBT people for much of the 20th century in western countries (proposition 8 would be an example of direct democracy), etc.