Inquisitor Pedro de Arbues was assassinated by a group of men while attending Mass in 1485 in Zaragoza, despite wearing chainmail under his clothes. The conversos (converted Jews) there were none too happy about him being around as he had already condemned several individuals; they had already made one attempt to kill him (hence the armor). Several conversos were condemned and executed for complicity in this plot (who knows how many of them were actually guilty, but the assassins themselves were definitely conversos).

The public outrage at the slaughter of a priest at mass solidified public opinion against the conversos, who were persecuted in large numbers in the coming decades under the direction of the Inquisitor General Torquemada. The Spanish Inquisition at this point was still relatively new (it had been founded in 1478) so this was an important moment in establishing the necessity of their initial function (finding practicing Jews among the newly baptized converso community- the Inquisition did not really focus on Protestant-style heretics until the mid-sixteenth century).

So, it was made clear early on that murdering an inquisitor would be punished with extreme brutality, and of course those who were being questioned would not really have the opportunity to attack their inquisitor while they were under arrest. Finally, I will note that accusations of nobles were relatively rare (especially at the close of the fifteenth century) because so few of them had Jewish blood, and those that did were still mostly of Old Christian stock. Merchants, artisans, and other types of 'middle class' individuals were the most frequent subjects of inquisitorial trials.

Can't remember where I originally read about the assassination of Arbues, probably Henry Kamen's "The Spanish Inquisition" book. The background information here at least comes from that work.