The 1999 book Khomeini: Life of the Ayatollah at page 280 says:
Khomeini believed that anyone who took up arms, directly or indirectly, against the Islamic government should suffer the death penalty. Whereas in defence of his arguments Montazeri cited examples of the clemency the Prophet had shown towards his enemies,[cites to reference 22 of chapter 14] to Khomeini it was a religious duty to follow the example of the Prophet's decisive action against the Jews of the Bani Qureizah, 700 of whom were, on a single day, beheaded for constant plotting against Islam. [cites to reference 23 of chapter 14]
However, the above had no indication of being related to Al-Quds Day.
Another answer refers to Khomeini's 08 August 1979 statement. However, this is not what the second reference in the OP is quoting from.
Instead, the German reference is going through chronologically the days starting with 08 August 1979.
Then is stated:
Am Freitag, dem 17.8.1979, hatten allein in Teheran 3,5 Millionen Menschen demonstriert. Laut Ettelaat sollen in den iranischen Provinzen ebenfalls einige Millionen Menschen aufmarschiert sein und tausende israelische und amerikanische Fahnen verbrannt haben. Nach den Demonstrationen meldete sich Khomeini noch einmal zu Wort:
[On Friday, 17.8.1979, 3.5 million people had demonstrated in Tehran alone. According to Ettelaat, a few million people were also deployed in the Iranian provinces, burning thousands of Israeli and American flags. After the demonstrations, Khomeini said:]
...
Imam Ali ist unser Vorbild. Er zog sein Schwert gegen die Verschwörer. Es ist überliefert, dass er siebenhundert Juden an einem Tag tötete. Auch der Imam der Muslime war rachsüchtig. Wenn es Zeit fürs Erbarmen ist, gibt es Erbarmen. Wenn es aber die Zeit der Rache ist, dann gibt es Rache. Uns geht es nicht um Ansehen im Iran, der islamischen Welt und im Ausland, wir wollen und werden nach göttlichem Willen handeln. Die Verschwörer sind Ungläubige. Auch die Verschwörer in Kurdistan sind Ungläubige. Die Regierung, die Sicherheitskräfte, die Armee müssen mit Härte auf sie reagieren. Falls sie Kompromisse schließen wollen, werden wir hart gegen sie vorgehen. Jeder Kompromiss hat Grenzen. Wir werden nicht zulassen, dass die Interessen der Muslime vernachlässigt werden. Die für die Revolution Verantwortlichen sind verpflichtet, alle Zeitungen zu verbieten, die gegen das Ziel der Revolution handeln. Autoren und Verantwortliche der Zeitungen, die sich gegen die Revolution stellen, müssen verurteilt werden.
[Imam Ali is our model. He drew his sword against the conspirators. It is surrendered that he killed seven hundred Jews in one day. The Imam of the Muslims was also vindictive. When there is time for mercy, there is mercy. But if it is the time of revenge, then there is revenge. We are not interested in Iran, the Islamic world and abroad, we want and will act according to God's will. The conspirators are unbelievers. The conspirators in Kurdistan are unbelievers. The government, the security forces, the army must react with hardship to them. If they want to make compromises, we will go hard against them. Every compromise has boundaries. We will not allow the interests of the Muslims to be neglected. The leaders responsible for the revolution are obliged to ban all newspapers which are against the goal of the revolution. The authors and those responsible for the newspapers who oppose the revolution must be condemned.]
So yes Khomeini said one should emulate Imam Ali's killing of 700 Jews, but this was not said in the sense that people should be killed on account of simply being Jewish.
