I have looked through that article, it's not short and it's not exactly easy to read, but the most significant point is that most of the material is from the 15th to 17th centuries and it would appear that by the beginning of the 19th century the Inquisition had lost much of its power.
>Towards the close of the eighteenth century various documents show that all ideas of resistance and all pleas of exemption had been abandoned. The Holy Office submitted to ordinary and extraordinary exactions and the Suprema warned the tribunals that the assessments were wholly in the hands of the royal officers and that it had no cognizance of the matter. The calls were frequent and heavy, as when, in 1794, four per cent, was levied on all salaries of over eight hundred ducats, and three months later a demand was made of one-third of the fruits of all benefices and prebends, which was meekly submitted to and statements were obediently rendered.<
>The times were adverse to privilege, however, and in 1805 the Captain-general of Catalonia sent a circular to all the towns stating that familiars were not exempt. The magistrates accordingly compelled them to furnish quarters and beasts of burden, and, when the tribunal complained to the captain-general and adduced proofs in support of its claims, he responded with the decrees of 1729 and 1743, which he assumed to have abrogated the exemption and he continued to coerce the familiars. The same process was going on in Valencia and, when that tribunal applied to Barcelona for information and learned the result, it ordered its familiars to submit under protest. Then followed a royal cédula of August 20, 1807, limiting strictly what exemptions were still allowed;<
>This hostility continued to the last, even though the decadence of the Inquisition in the eighteenth century diminished so greatly its powers of oppression. A defender of the institution, in 1803, commences by deprecating the hatred which had pursued it from the beginning; even in the present age, he says, of greater enlightenment, there is crass ignorance of its essential principles and a mortal opposition to its existence.<
This would suggest that abolition should have been fairly straightforward and that if the abolition did cause hostility it may have been badly handled. Curiously, the Inquisition was revived at the Restoration, though apparently with reduced powers.
regards,
Susan