I'd agree with the overall thrust of your portrayal of the riots, and will add some context to it. Before coming to the riots, a few points on Shmuel HaNagid, or Samuel ibn Nagrillah as he's known in Muslim sources. Ibn Nagrillah was a famous Jewish scholar and poet, fluent in Hebrew and Arabic. On top of that he has also been described as one of the most influential Jews in Muslim Spain, as he served as vizier to the Granadan kings. This included him commanding the Muslim army as top general of the Granadan army. What's important for your question here is the particular position first of Jewish courtiers, being dependant on the ruler's protection and goodwill despite the power they could wield; and second the exceptional position of Ibn Nagrillah the elder even among Jewish courtiers. All this might go some way to explain a building up of ressentiments in the population against a Jewish official in this position.

I managed to somehow delete an earlier text I just wrote on this, so will now focus on the main events regarding the riot itself. Samuel ibn Nagrillah was succeeded after his death around 1055/6 by his son Joseph or José as vizier of Granada. As the main sources on José come from Muslim scholars, including a descendant of the Granadan rulers, we should keep this bias in mind (he is tellingly often referred to as “el puerco”, the swine, in sources). Early on, we see various claims and even death threaths against José ibn Nagrillah. Later sources also include claims of José using large bribes and gifts as to oust rival Muslim viziers (which ideas supposedly goes back to Samuel); and of overall bad behaviour, ie. him lending money to one of the king's sons only to then accuse the son of excessive spending in front of the king.

Coming to the riots of 1066 themselves, I'll quote a sources that gives some further reasons behind it (my translation, from Molina Lopez, cf below):

During the reign [of Badis b. Habbus, the Granadan ruler] the Jews suppressed the Muslims until the latter made known their perversity [to Badis], which moved him to castigate his [ibn Negrella's] supporters and killing a great number of his followers. Their motivation was that this cursed one [ibn Negrella] tried constituting a Jewish kingdom and plotted secretly with the ruler of Almería Ibn Sumadin, so that he would enter Granada and Jew would establish himself in Almería. This conspiracy was heard by the Sinhaya who, together with the population, entered the Jew's house; he had hidden himself in a storage place for charcoal [“carbonería”] begriming his face, but they recognized him, and killed and crucified him at the city gates. On this same day the necks of many Jews were cut and they were brought from their houses.

In another source numbers of killed are given at more than 3000 Jewish people. This is one of the more polemical descriptions, and there are more neutral ones. But I think it's interesting here as to see the accusations brought against ibn Nagrillah as well as possible motivations behind the riots. The supposed conspiracy by the vizier is here extended to ibn Nagrillah trying to form a Jewish kingdom with the help of the ruler of Almería – in itself an improbable idea, this is also similar to ideas we see with later riots against Jews in Iberia.

Mentions in other sources also show that the properties of the killed were then confiscated, adding an economical dimension to the popular jealousy/anger with ibn Nagrillah's supposed misconduct. This is again a pattern we see with many later medieval progroms and riots against Jews also in other (Christian) European countries, where a city's Jewish population is used as a scapegoat, and their properties are then taken over, often with the ruler's approval. As I mentioned in the beginning even anger with ibn Nagrillah the younger could be connected with longer-term jealousy in the population regarding his father's exceptional political influence.

To finish, this quote by Jonathan Decter gives a good overview of the Jewish courtiers' highly complicated situation:

Jews were functional not because they often shared the political and intellectual commitments of the ruling culture but also because they could mediate between their home governments and foreign (including enemy) kingdoms. [...] As financiers, Jewish courtiers were appreciated as supporters of the state. As tax farmers, they were appreciated by rulers but often resented by the masses, which might also have been by design. One need not be a cynic to view the celebrated role of the Jewish courtier in pragmatic or utilitarian terms.

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Sources:

• Jonathan P. Decter,Before Caliphs and Kings: Jewish Courtiers in Medieval Iberia, in: The Jew in Medieval Iberia (1100-1500), ed. Jonathan Ray.

• Emilio Molina López, Los Banu Sumadih de Almería (s. XI) en el Bayan de Ibn Idari, in: Andalucía Islámica. Textos y estudios, I, p. 138-39.

• El siglo XI el 1a Persona. Las "Memoriales" de Abd Allah, último rey zirí de Granada, destronado por los almorávides (1090), transl. by Evaristo Levi-Provincal & Emilio García Gómez, pp. 111-13.

Edit: Modified a phrase in the translation.