The Inquisition had nothing to do with the forced conversions. Strictly speaking the Inquisition had no jurisdiction regarding none Christians, Jews only appeared in Inquisition trials as witnesses most often against the defendant. In any case most of the forced conversions took place well before Isabella during a period of riots in the 1350s. And it was not a government sponsored action either, but a spontaneous serious of peasant revolts which had to be put down by royal troops.
What are you talking about? Wasn't Spain ruled mostly by the Muslims in the 1350s? Ferdinand and Isabella were the first Spanish Royalty to rule "Spain" in several hundred years, uniting the country and kingdoms with their marriage not long before Columbus' little boat trip. There were small Christian kingdoms in the northern part of the country, always at the mercy of the much stronger Moors, who ruled central and southern Spain for around 700 years.
There certainly may have been the riots and forced Christianization that you speak of, but they would have been in reaction to living in the shadow of Jihad. Ya ain't paranoid if they really are out to kill (or convert) you.
Context matters.