Most of the negative reports I have read of the Inquisition involved their terrible treatment of Jews. Jews were forced to convert to Catholicism, and the Inquisition severely punished those whose conversions were not genuine.
Precisely so, and the number of such prosecutions and executions was remarkably small.
As for forcing conversions, it has to be remembered that this was allowed, and enthusiastically encouraged. Indeed, the first inquisitor himself, Torquemada, was the son of a converso.
In other lands when Jews were massacred or expelled they were rarely given a choice, the point being to get rid of the people. In Spain everthing was done to keep the people but expunge the religion. Spain even encouraged the return of expelled Jews, and mandated restoration of their property, on the condition that they converted.
Iberia (Spain and Portugal) had more Jews in the middle ages than anywhere else on earth probably, estimates run to 10% of the population. Nearly all were permitted to stay and convert (in Castile and Aragon) throughout the fifteenth century. The expulsion of the Jews was just the last part of a long-running process managed by the Spanish Church, to integrate the populations put in their hands by the reconquista. Of the Jewish remnant in 1492, 2/3 to 3/4 chose to convert and remain. The Spanish today are, overall, genetically very Jewish, of the Sephardic sort.